AUTOIMMUNE

PROTOCOL
Everything you need to jump-start your
healing with the AIP today.

BY DR. SARAH BALLANT YNE, PhD W W W.T H E PA L E O M O M . C O M 1

1
 THE AUTOIMMUNE
PROTOCOL
Everything you need to jump-start your healing with the AIP today.
BY DR. SARAH BALL ANT YNE, PhD

Copyright 2019© the Paleo Mom LLC

No part of this publication may be reproduced, distributed, or sold in whole or in part, by any means,
with or without financial gain, without the prior written consent of the author. The information
contained in this book is for educational purposes only.

Disclaimer
Always consult your healthcare provider before making any diet or lifestyle changes. The recommen-
dations in this book are not intended to diagnose, treat, cure, or prevent any disease. By reading this
book, you agree that The Paleo Mom LLC is not responsible for your health relating to any information
presented in this book. This book contains affiliate links to products or services on external websites.
This means that The Paleo Mom LLC receives a small commission when purchases are made at these
sites without any increased cost to the buyer.

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 TABLE of CONTENTS
PART 1
5
Click on each icon
Understanding Autoimmunity
to go to each part!

PART 2
32 The Autoimmune Protocol

PART 3
110 Practical AIP

PART 4
143
Reintroduction & Troubleshooting

PART 5
176 Meal Plans & Recipes
187 Basic Recipes
210 Meal Plan Recipes 1
230 Meal Plan Recipes 2
242 Meal Plan Recipes 3
269 Meal Plan Recipes 4
293 Desserts
303 AIP Resources

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 ABOUT THE AUTHOR
Dr. Sarah Ballantyne, PhD
Award-winning public speaker, New York Times bestselling
author and world-renowned health expert, Dr. Sarah
Ballantyne, PhD (aka The Paleo Mom) believes the key to
reversing the current epidemics of chronic disease is scientific
literacy. She creates educational resources to help people
regain their health through diet and lifestyle choices informed
by the most current evidenced-based scientific research.
Dr. Sarah earned her doctorate degree in medical biophysics at
the age of 26 and spent the next four years doing research on
critical care medicine, innate immunity, gene therapy and cell
biology, earning a variety of awards for research excellence
along the way. 

Sarah’s transition from academic researcher to stay-at-home mom to award-winning and

internationally-recognized health advocate and educator was driven by her own health journey,
which included losing 120 pounds and using both diet and lifestyle to mitigate and reverse a dozen
diagnosed health conditions. Sarah’s talent for distilling scientific concepts into straight-forward
and accessible explanations form the foundation of her work and her dedication to improving
public health.

Learn more by checking out Sarah’s website, podcast and books. You can also find Dr. Sarah
on Instagram, Facebook, Pinterest and Twitter or join her private Facebook Community here.

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by Dr. Sarah Ballantyne, PhD
 PA R T O N E

Understanding Autoimmunity

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 THE EPIDEMIC OF
AUTOIMMUNE DISEASE
Chronic illness is epidemic in our society. More than half of all Americans take two or more prescription
drugs, and about one-fifth of us take at least five different daily medications prescribed by our doctors.
This isn’t normal. We’re not supposed to be so sick that we need multiple medications to get us through
each day. We’re not supposed to be this unhealthy.

Not that long ago, people were substantially healthier. Incidences of just about every chronic health
problem—things like cardiovascular disease, obesity, diabetes, asthma, allergies, autoimmune disease,
and cancer—are on the rise and have been for several decades. Rates of chronic health problems are so
high that nowadays more of us are unhealthy than are healthy.

In fact, 85% of healthcare spending is for diagnosis and management of

chronic disease.
Autoimmune diseases may account for as much as half of all chronic diseases suffered by Americans
today. The American Autoimmune Related Diseases Association (AARDA) estimates that 50 million
Americans suffer from at least one autoimmune disease. In comparison, approximately 12 million
Americans suffer from cancer and 25 million from heart disease. These numbers are not only staggering
in their own right, but the prevalence of autoimmune disease is increasing.

THE COST OF AUTOIMMUNE DISEASE

# PEOPLE ESTIMATED DIRECT

HEALTH CARE COSTS
RESEARCH
AFFECTED IN THE U.S.

$ $$$
CANCER 12 MILLION $93 BILLION
$ $6.1 BILLION
$ $$$

HEART DISEASE 25 MILLION $273 BILLION $$$ $2.4 BILLION $$$$

AUTOIMMUNE DISEASE 50 MILLION

$100 BILLION
( likely underestimated)
$ $591 MILLION $

The National Health Institues of health conservatively estimates the annual health care costs sclerosis, rheumatoid arthritis, psoriasis and scleroderma) are estimated to total
of autoimmune disease to be $100 billion. $70 billion annually.

The true cost of autoimmune disease is probably much much higher. The annual Despite the prevalence of autoimmune disease, research in the field is embarassingly
direct health care costs of just seven of the hundred-plus known autoimmune underfunded. AARDA evaluated National Insitutes of Health research funding in 2003
diseases (Chron’s disease, Ulcerative colitis, systemic lupus erythematosus, multiple and found that less $600 million was spent on autoimmune disease that year, compared
with more than ten times that amount spent on cancer.

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 Autoimmune disease is still greatly underdiagnosed and the true number of people afflicted remains
unknown: it is estimated, for example, that celiac disease has been diagnosed in only 5% of those who
actually suffer from it. This is, in part, because autoimmune disease can be challenging to diagnose as it
often presents as a collection of vague symptoms (such as fatigue, headaches, and muscle or joint aches).
Too often these symptoms are dismissed as signs of getting insufficient sleep, working too hard, being
stressed, being over or underweight or aging.

In fact, a survey performed by AARDA showed that the majority of patients later
found to have serious autoimmune conditions had a difficult time obtaining a diagnosis:
45% of them were labeled hypochondriacs in the earliest stages of their illnesses.
Many people struggle with symptoms, going from specialist to specialist and enduring test after test,
to no avail—at least until the disease has progressed to the point at which the symptoms are severe,
predictable, and fit into a pattern consistent with a specific autoimmune disease. Unfortunately most
of the time, there is no single test that can definitively determine whether you have an autoimmune
disease. Rather, doctors must piece together clues from medical histories, symptoms, physical exams,
laboratory tests (most commonly blood tests), radiography results, and biopsies.

As challenging as it is to diagnose, autoimmune disease is

AUTOIMMUNE DISEASE even harder to treat. There is no cure for autoimmune dis-
IS ON THE RISE ease. Depending on the specific autoimmune disease and
severity of symptoms, patients may be prescribed immuno-
400
Incidence of immune disorders (%)

suppressant drugs (such as corticosteroids and DMARDs

like methotrexate and infliximab), hormone replacement
300 therapy (such as thyroid hormones or insulin), or various
medications for symptom management. Patients may also
undergo surgeries, physical therapy, occupational therapy,
200 or seek out experimental or alternative health treatments.

Autoimmune diseases run in families, with women being

100 more than three times as likely to develop one as men. Once
1950 1960 1970 1980 1980 1990 2000
you have developed an autoimmune disease, you are at much
Multiple scleorsis Asthma
Crohns disease Type 1 Diabetes greater risk of developing additional autoimmune diseases.
Although asthma is an immune disorder, not an autoimmune disorder, In addition, several chronic diseases are frequently
it may have similar causes.
J.F. Bach “The effect of infections on susceptibility of autoimmune and allergic diseases.
co-morbid with autoimmune disease. (Co-morbidity is defined
” New England Journal of Medicine 347 (Sep 19, 2002): 911-920. Copyright 2002
Massachusettes Medical Society. Reprinted with permission from Massachusetts Medical Society.
as the simultaneous presence of two chronic diseases or
conditions in a patient.) These include: cholangitis (infection
or inflammation of bile duct system and/or gallbladder), chronic fatigue syndrome, eczema, fibromyal-
gia, and polycystic ovary syndrome. Fibromyalgia and chronic fatigue syndrome are suspected autoim-
mune diseases themselves.

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 WHAT IS AUTOIMMUNE
DISEASE?
There are more than one hundred confirmed autoimmune diseases and many more diseases that are
suspected of having autoimmune origins. The root cause of all autoimmune diseases is the same: our
immune system, which is supposed to protect us from invading microorganisms, turns against us and
attacks our proteins, cells, and tissues instead. Which proteins, cells, and tissues are attacked determines
the autoimmune disease and its symptoms. In Hashimoto’s thyroiditis, the thyroid gland is attacked.
In rheumatoid arthritis, the tissues of your joints are attacked. In psoriasis, proteins within the layers of
cells that make up your skin are attacked.

How does the immune system get so confused that it starts to attack our own bodies? It turns out that
autoimmunity, the ability for the immune system to attack native tissues, is a relatively common
accident. In fact, about 30% of people have measurable levels of autoantibodies (antibodies that bind to
some protein in our bodies instead of, or in addition to, a foreign protein, called an antigen) in their blood
at any given time. In fact, this accident is so common, that our immune system has several failsafes for
identifying autoimmunity and suppressing it. What occurs in autoimmune disease isn’t just the accident
of autoimmunity, but also failure of the immune system failsafes, stimulation of the immune system to
attack, and the build 500 up of enough damage in cells or tissues within the body to manifest as
symptoms of a disease.

This confluence of events that culminates in autoimmune disease is a result of the

interactions between your genes and your environment—a perfect storm of factors that
cause the immune system to be unable to distinguish self (you) from invader (not you).

BRAIN THYROID
Multiple Sclerosis Thyroiditis
Guillaun-Barre Syndrome Hasimoto’s Disease
Autism Graves Disease

BLOOD
Leukemia BONES
Lupus Erythematosus Rheumatoid Arthritis
Hemolytic Dysglycemia Ankylosing Spondylitis
Polymyalgia Rheumatica
COMMON
GI TRACT AUTOIMMUNE
Celiac’s Disease MUSCLES
Crohn’s Disease DISEASES Muscular Dystrophy
Ulceratic Colitis Fibromyalgia
Diabetes Type 1

NERVES SKIN
Peripheral Neuropathy Psoriasis
Diabetic Neruopathy Vitiligo
Eczema
Scleroderma

LUNGS
Fibromyalgia
Wegener’s Granulomatosis

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 THE IMMUNE SYSTEM PALEO PRINCIPLES 81

AT WORK THE IMMUNE SYSTEM AT WORK

TONSILS AND ADENOIDS T HY M US GL A ND

As an early warning system, tonsils T cells mature in the thymus,
and adenoids can detect pathogens where they learn how to
and food allergens especially quickly differentiate between our own
and activate the immune system. cells and foreign invaders.

MALT SPL EEN

Other barrier tissues, like sinuses, The spleen stores red blood cells,
lungs, bladder, and vagina, also immune cells like macrophages, T
contain lymphatic tissue acting as cells and B cells, and platelets for
a sentinel for early detection of when needed. It also filters the
infections, referred to as mucosa- blood, removing old red blood cells
associated lymphoid tissue (MALT). for degradation.

LYMPH NODES G A LT
Working like biological filter stations, A huge proportion of the immune
lymph nodes contain different immune system is housed in the tissues
cells that trap pathogens and surrounding the gut, referred to as the
activate the production of specific gut-associated lymphatic tissue (GALT).
antibodies in the blood.

B O N E MA RRO W
Most immune cells are produced
in the bone marrow and then
released into the bloodstream to
reach other organs and tissues.

Pathogen Antigen
Antimicrobial Macrophage
molecules
B cell
receptor T cell
Infected cell
Dendritic cell recognizing
Monocyte displaying
B cell a specific
antigen
antigen

Cytokines and Activated B cell

other inflammatory (plasma cell)
proteins T cell attacking
infected cell
Macrophage

Antibody
Memory Memory
Blood vessel B cell T cell

Neutrophil

INNATE IMMUNE SYSTEM: ADAPTIVE IMMUNE SYSTEM:

The innate immune system acts as a sentinel near entry When the innate immune system presents antigens to the
points to the body, like skin, sinuses, lung tissues, and the adaptive immune system, it kicks in to mount a targeted
gut. The system includes antimicrobial molecules (like the attack against the specific invader. B cells produce
complement system) and phagocytic cells (cells that ingest antibodies that bind to antigens, specific components unique
and destroy pathogens, but also can alert the adaptive to a given invader, and destroy the invader or mark it for
immune system about what they’ve found), like dendritic cells attack by other cells. T cells recognize antigens. Some T
and macrophages. When the innate immune system gets cells help activate B cells, and others attack infected cells
activated, sentinel cells produce chemical messengers of directly. T and B cells spawn “memory” cells that patrol the
inflammation (cytokines) that attract other immune cells to body and allow for a faster adaptive immune response on
the area from blood vessels, like monocytes and neutrophils. subsequent exposure to the same antigen.

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 HOW GENES PREDISPOSE
US TO AUTOIMMUNE DISEASE
The genetic factors at play are complex. In contrast to many inherited diseases (in which mutations
in a single or small number of gene variants directly cause the disease, such as sickle cell anemia or
cystic fibrosis), many different gene variants collectively increase vulnerability or susceptibility to
autoimmune disease, and unfortunately only a small number of them have been identified.

In general, your genetics accounts for approximately one third of your risk
for autoimmune disease. There are at least 68 different gene variants
identified to each increase risk of autoimmune disease.
What is a gene variant? Let’s start with proteins. Proteins, the building blocks of life, are made from
long chains of amino acids (the basic structural units of proteins). While approximately 500 different
amino acids have been identified in various life forms, only twenty are used to build every single type
of protein in the human body. Three additional amino acids are found in the human body and can be
incorporated into proteins after being built (by a chemical reaction called post-translational modifi-
cation). Various combinations of amino acids are strung together in chains anywhere from twenty to
more than two thousand amino acids long. As you can imagine, there are many ways to string twenty
different amino acids together. This is how twenty simple building blocks form all the proteins in your
body, from the components of the cells of your organs to the hormones that circulate in your blood.

A gene, which is made up of DNA, is basically a detailed map

for creating a specific protein within a cell. DNA is made up
of a long chain of nucleotides, arranged in base pairs (there
are only four nucleotides that make up DNA: adenine [A]
which always pairs with thymine [T], and guanine [G] which
always pairs with cytosine [C]), which gives it its signature
double-helix structure. Every amino acid is encoded by a
unique series of three nucleotides, which is how the DNA map
provides the information to create protein. Organelles within
the cells “read” the DNA, first “transcribing” DNA into mes-
senger RNA, then “translating” mRNA into protein. Humans
have about 23,000 genes, meaning that our cells can produce
about 23,000 different proteins.

THE AUTOIMMUNE PROTOCOL

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11 by Dr. Sarah Ballantyne,PROTOCOL
PhD
by Dr. Sarah Ballantyne, PhD
 The most common type of genetic variation among people is called a single nucleotide polymorphism
(SNP, pronounced “snip”). A SNP means that a single nucleotide in a gene is swapped out for a different
one. For example, a SNP may replace a cytosine with a thymine in a certain strand of DNA. This then
means that a single amino acid is swapped out for a different amino acid in the protein that is encoded
by this particular gene. Just changing one amino acid, doesn’t make a huge difference to the protein
structure—the same protein is still made—but it can make a subtle difference to the function of that
protein, perhaps changing how active an enzyme is or how that protein might bind with its receptor.

When specific SNPs appear in a non-significant proportion of the population, we call it a gene variant.
Gene variants are inherited from one or both of your parents.

The vast majority of gene variants linked to autoimmune disease risk encode
proteins with important roles in immune function.
For example, the human leukocyte antigen (HLA) genes encode the major histocompatibility complex
(MHC) proteins in humans. When an inflammatory cell (specifically, an antigen-presenting cell like a
macrophage or a dendritic cell) eats a foreign invader (a process called phagocytosis), a protein
fragment from the invader is left on the surface of the inflammatory cell’s own membrane. This pro-
tein fragment is bound to a special protein embedded in the cell’s surface, yes, the MHC (specifically
MHC Class II). The MHC’s job is to present antigens from foreign invaders the cell has already eaten
to the adaptive immune system. When this inflammatory cell meets a type of white blood cell called a
helper T cell, the helper T cell recognizes the antigen presented in the MHC and is activated. Once
activated, the helper T cells start to divide and produce proteins that activate B cells (the type of cell
that produces antibodies) and other types of T cells as well as other immune cells, triggering a
response of the adaptive immune system (also called acquired immunity or specific immunity). At least
50 variants of HLA genes have been linked to increased autoimmune disease risk, due to alterations in
the function of the MHC proteins, fundamentally impacting how the immune system learns to attack
a specific foreign invader.

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 Gene Variants Linked to Autoimmune Disease

At least 68 gene variants have now been associated with increased risk of various
autoimmune diseases. The following is a sample of the most common and best
understood genes in terms of autoimmune disease risk.

MT H F R-C 667T and MT H F R-A 1298C are linked to type 1 diabetes, Hashimoto’s
thyroiditis, Graves’ disease, rheumatoid arthritis, vitiligo, multiple sclerosis, Alzheimer’s
disease* and schizophrenia* (also cardiovascular disease, renal disease, neurodegenerative
disease, osteoporosis, and cancer).

H L A-B 8 is linked to Grave’s disease

H L A-B 27 is linked to ankylosing spondylitis, postgonococcal arthritis, acute vanterior

uveitis, reactive arthritis (Reiter’s syndrome), seronegative spondyloarthropathy, iritis,
psoriatic arthritis, Crohn’s disease, ulcerative colitis, and ulcerative colitis–associated
spondyloarthritis

H L A-B 47 is linked to 21-hydroxylase deficiency

H L A-D R 2 is linked to systemic lupus erythematosus, chronic Lyme disease

H L A-D R 3 is linked to autoimmune hepatitis, primary Sjögren syndrome, and

Grave’s disease

H L A-D R 3 and H L A-D R 4 are linked to type 1 diabetes mellitus, and

Hashimoto’s thyroiditis

H L A-D R 4 is linked to chronic Lyme disease

H L A-D Q 2 and H L A-D Q 8 are linked to celiac disease, Hashimoto’s

thyroiditis, and primary Sjögren syndrome

H L A-D Q 5 is linked to scleroderma

H L A-D Q 7 is linked to Hashimoto’s thyroiditis

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 ENVIRONMENTAL TRIGGERS
OF AUTOIMMUNE DISEASE
The other two thirds of your risk for autoimmune disease comes from your environment.

Environmental triggers are also complex and include, but are not limited to: exposure to chemicals,
pollutants, and toxins; bacterial, viral, fungal, and parasite infections (whether in the past or present);
stress (chronic and acute); hormones (whether regulated by the body or pharmaceutically); diet
(including food sensitivities but also the influence of diet on gut health, hormone regulation, and
immune system function); micronutrient deficiencies; drugs; weight gain; fetal blood cells; and UVB
radiation exposure.

While most autoimmune diseases are caused by several elusive environmental factors, for some the
specific environmental factor is known. For example, celiac disease is triggered by consumption of
gluten; solvent exposure can cause systemic sclerosis; and smoking can contribute to the development
of seropositive rheumatoid arthritis.

Increased intestinal permeability (a.k.a. leaky gut) and gut dysbiosis (imbalance in
the microbial community residing in our gut which can include altered species, relative
quantities or location)--which are themselves closely tied to diet and lifestyle factors--
are contributors to, and potential necessary preconditions for, autoimmune disease.

The Gut Barrier

Gut is the colloquial term for the gastrointestinal tract (also called the GI tract, digestive tract, digestive
tube, or gastrointestinal system), an organ system composed of the esophagus, the stomach, and both
the small and large intestines. It also happens to be the largest barrier between our bodies and the out-
side world (the contents of your gut are technically outside of your body) The gut has the very tricky job
of letting nutrients into the body while keeping bacteria, viruses, parasites, other pathogens and toxins
from entering the body. To achieve this function, the gut is equipped with an array of physiologic defense
mechanisms, including mucus, digestive enzymes, acid, and about 80% of our immune system! When the
gut barrier becomes more permeable, or leaky, pathogens and toxins can enter the body in an uncon-
trolled way. This activates the immune system, causing both generalized (body-wide) inflammation and
targeted immune activation (the adaptive immune system).

Increased intestinal permeability is present in every autoimmune disease in which its presence has been
evaluated, including rheumatoid arthritis, ankylosing spondylitis, inflammatory bowel disease (Crohn’s
and ulcerative colitis), celiac disease, multiple sclerosis, and type 1 diabetes. It may seem obvious that a

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 leaky gut is present in celiac disease, Crohn’s disease,
and ulcerative colitis, which are, after all, pathologies
of the gut! But in these three autoimmune diseases,
increased intestinal permeability has been shown to
precede development of the disease.

Perhaps somewhat alarming, a handful of studies have

shown increased intestinal permeability in the healthy
relatives of those with autoimmune diseases, as in the
case of ankylosing spondylitis. These people proba-
bly have autoimmune susceptibility genes in common
with their sick aunt, cousin or sister. Having a leaky
gut—which may be because of diet and lifestyle factors
shared by family members—should be a big red flag.

Environmental Toxins and Autoimmune Disease

A variety of environmental toxins increase risk of autoimmune disease,

including cigarette smoke, heavy metals, pristane, silica dust, ultraviolet
radiation, pesticides and even some prescription drugs! In fact, 38 drugs
linked to lupus (called drug-induced lupus erythematosus), including
hydralazine (a blood-pressure medication), procainamide (used to treat
cardiac arrhythmias), and isoniazid (an antibiotic used to treat tuberculosis).

The Gut Microbiome

Gut dysbiosis is also a major contributor to autoimmune disease, again, present in every autoimmune
disease in which its presence has been investigated.

The gut is a biological niche, home to a diverse array of microbes that influence nearly all aspects of
human biology through their interactions with our bodies. Our gut microbiota help us digest food, pro-
duce chemicals that improve the health of the cells that form the gut barrier, and directly regulate the
immune system, and they can even influence brain health by producing neuroactive chemicals that are
absorbed into the bloodstream and travel to the brain. A healthy diversity of the right kinds of microor-
ganisms in the gut is one of the most fundamental aspects of good health.

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 PALEO PRINCIPLES 69

THE LEAKY GUT GUIDE

WHAT IS A LEAKY GUT? Micro-
organisms
A leaky gut occurs when the
cells that form the intestinal Gluten
wall or the tight bonds
between them are damaged. Toxins
When this happens, the gut
barrier loses its ability to
regulate which molecules Healthy Leaky and
cross into the body. inflamed

GUT BARRIER

BLOOD-
STREAM

DEVELOPMENT OF A LEAKY GUT

1. A healthy gut barrier 2. Minor intestinal 3. Prolonged 4. The passage of more 5. Severe intestinal
is resilient to some permeability due to gut minor intestinal and more large molecules permeability
stressors and toxins. barrier defects results permeability into the body leads to develops and results
It is normal for some in an increased passage results in an inflammation and immune in overactivation of
large molecules to cross of large molecules into exaggerated system activation, which may the immune system,
into the body, and it’s the body; however, immune response, result in the destruction cell death, tissue
the immune system’s job homeostasis (the causing damage of tight junctions and damage, autoimmune
to deal with them while maintenance of a stable to the gut enterocyte cell death, disease, multi–organ
remaining well regulated. environment inside and barrier. leading to even greater system disorder,
This is called mucosal or outside the cells) is passage of large molecules. and chronic health
immune tolerance. maintained. This becomes a vicious cycle. problems.

WHAT CAUSES A LEAKY GUT? SYMPTOMS OF A LEAKY GUT

• Advanced glycation • Infections GASTROINTESTINAL NEUROLOGICAL SKIN SYMPTOMS: OTHER SYMPTOMS:

end-products SYMPTOMS: SYMPTOMS:
• Lipopolysaccharides Acne Aches and pains
• Antibacterial Abdominal pain ADD/ADHD
• NSAIDs (such as Dry skin Autoimmune disease
peptides
aspirin and ibuprofen) Bloating Anxiety
Eczema Difficulty maintaining
• Antibodies
• Stress Burping Brain fog a healthy weight
Hives
• Antigens
• Toxins Gas Depression Food sensitivities/
Itchy skin
• Dietary proteins allergies
• Undigested food Irregular stools Fatigue, especially
and peptides Psoriasis
particles (constipation or after eating Joint pain
• Enzymes diarrhea) Rashes
Headaches Symptoms of
Nausea/vomiting Rosacea malnutrition
Insomnia
Reflux/heartburn

DISEASES LINKED TO LEAKY GUT

Ankylosing spondylitis Chronic heart failure HIV/AIDS Multiple sclerosis Rheumatoid arthritis

Asthma Chronic inflammation Inflammatory joint Non-alcoholic fatty liver Stroke

disease disease
Atopic dermatitis Crohn’s disease Type 1 diabetes
Insulin resistance Obesity
Cardiovascular disease Depression Type 2 diabetes
Irritable bowel syndrome Psoriatic arthritis
Celiac disease Eczema Ulcerative colitis
Multiple organ failure Psychological conditions
Chronic fatigue syndrome Food allergy

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 Our gut bacteria also directly control the integrity of the gut
barrier by regulating important proteins that bond together the
cells that form the gut barrier. These effects aren’t limited to
the gut either: recent studies have shown that our gut bacteria
can regulate the permeability of epithelial barriers elsewhere in
the body, including the blood-brain barrier (yep, our gut bacteria
control how leaky the blood-brain barrier is). So, an essential
aspect of restoring gut barrier health is cultivating a healthy
and diverse gut microbial community.

The microorganisms in our guts also help to maintain the

delicate balance required by our immune systems, keeping
the various populations of immune cells in check and modulat-
ing their activity. Achieving a healthy balance in the immune
system is therefore also reliant on having a healthy gut micro-
biome. In fact, gut dysbiosis (an unhealthy gut microbiome) is
not only linked to intestinal autoimmune diseases such as ulcerative colitis, Crohn’s disease and celiac
disease, but also non-intestinal autoimmune diseases, including: Grave’s disease, multiple sclerosis, type
1 diabetes, systemic lupus erythematosus, and psoriasis, as well as the suspected autoimmune conditions
schizophrenia and autism spectrum disorder.

The composition of our gut bacteria is approximately 60% determined by our diet (they’re happiest when
we eat a high-fiber adequate-protein, high-omega-3, moderate-fat, high-phytochemical, nutrient-dense
diet like the Autoimmune Protocol), with the other 40 % determined by environmental exposures (like
antibiotics and heavy metal exposure), lifestyle (our gut bacteria are sensitive to our stress levels, sleep,
and activity), probiotic exposure (such as playing in the dirt or eating fermented foods), and our hormone
environment (such as our vitamin D status and insulin sensitivity).

Evidence is mounting that leaky gut and gut dybiosis are necessary preconditions
for autoimmune disease to develop.

What does that mean? In order to develop autoimmune disease, you must first have a genetic predispo-
sition to it, you must have a leaky gut and gut dysbiosis, and there must be a triggering event (such as
infection, toxin exposure, stress, or severe nutritional deficiency). Both gut barrier and gut microbiome
health are inextricably tied to our diet and lifestyle, and that’s good news! It means that we can change
what we’re eating and our lifestyle priorities to remove this autoimmune disease trigger.

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 LINKS BETWEEN GUT
BACTERIA AND HEALTH PALEO PRINCIPLES 73

LINKS BETWEEN GUT BACTERIA AND HEALTH

MOOD DISORDERS: OBSESSIVE COMPULSIVE DISORDER:
Bacteria in the gut activate neural pathways and Dysfunction of the gut microbiome, perhaps related to
central nervous system signaling systems. Gut dysbiosis, high stress and/or antibiotic use, is linked to OCD.
especially a lack of beneficial bacterial strains, is linked
to depression and anxiety, with more than a third of AUTISM:
depression sufferers also having a leaky gut. Autism often co-occurs with gastrointestinal
issues like leaky gut and irritable bowel syndrome.
SCHIZOPHRENIA:
Mice studies link a lack of normal bacteria with PARKINSON’S DISEASE:
changes in brain development and schizophrenic People suffering from Parkinson’s
behavior. Human infants born prematurely are have different microbial composition
known to lack biodiversity in their guts and be of the gut than healthy people.
at a higher risk of schizophrenia.

MULTIPLE SCLEROSIS:
CARDIOVASCULAR DISEASE: Dysbiosis and the resulting loss
Certain grain-loving bacteria are known of balance in gastrointestinal
to also convert L-carnitine, a protein immune responses are linked to the
rich in red meat, into an atherogenic development of MS and may explain
compound called TMAO, raising the risk of why MS symptoms can be mitigated
cardiovascular disease (see page 64). with therapeutic diets.

LIVER CANCER: ASTHMA AND ALLERGIES:

The same changes in microbial composition Low diversity of gut bacteria,
that are linked to obesity are known to especially early in life, is linked to
increase the risk of liver cancer. increased risk of asthma and allergies.

OBESITY: DIABETES:
Gut microbes can impact metabolism via Diabetics have lower levels of beneficial
signaling pathways in the gut, with effects strains of bacteria and skewed ratios of
on inflammation, insulin resistance, and different strains, with lower numbers of
deposition of energy in fat stores. A gut microbes overall. Some compositional
number of studies show specific microbial changes in gut microbiota appear to
patterns associated with obesity. scale with glucose levels—that is, the
higher a person’s glucose levels, the
INFLAMMATORY BOWEL fewer total microbes and the more
DISEASES: undesirable species of bacteria are likely
Abnormally high levels of certain to be found in that person’s gut.
undesirable strains of bacteria along
with dysregulated immune responses RHEUMATOID ARTHRITIS:
to gut microbes may trigger Studies have found a link between low
the development and continuing levels of probiotic bacteria and high
symptoms of both Crohn’s disease levels of undesirable bacterial strains
and ulcerative colitis. COLORECTAL CANCER: with autoimmune joint diseases like RA.
Lower levels of beneficial bacteria
IRRITABLE BOWEL SYNDROME: as well as higher levels of certain OTHER CANCERS:
There is a definitive link between sugar-loving microbes in the gut are Dysbiosis is linked to increased risk of
IBS and an overgrowth of bacteria linked to increased risk and growth gastric, esophageal, pancreatic, laryngeal,
in the small intestines (SIBO). rates of colorectal cancers. breast, and gallbladder carcinomas.

GOOD BAD
RIUM OCOCC OBACIL D I UM D I CCUS F OBAC
CTE CT U CT FF CO AE PYL TE
BA LO LA S LA
L I RI I O C AM R
O T R C
S

E
D

C
N

A
O

T
FI

IL
G

LI
CL

EN
UM
BI

18 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Diet Factors
Experts are increasingly recognizing that certain dietary
factors are also key contributors to autoimmune disease
(beyond their impact on gut health), placing these
autoimmune conditions in the same class of diet- and life-
style-related diseases as type 2 diabetes, cardiovascular
disease, and obesity. For example, celiac disease, multiple
sclerosis, dermatitis herpetiformis, and bullous pemphi-
goid have been definitively linked to gluten as an environ-
mental trigger. Case studies are beginning to suggest that
gluten sensitivity may be an important trigger for other
autoimmune diseases; in some instances, a gluten-free diet
is the only treatment necessary to achieve full remission.
Furthermore, the high prevalence of secondary (and
tertiary) autoimmune diseases suffered by celiacs supports
the concept that gluten is a trigger for other autoimmune diseases. Although the exact role that gluten
plays in most autoimmune diseases is elusive, the link between gluten sensitivity and increased
intestinal permeability is so compelling that many experts in the field believe that gluten sensitivity
may contribute to all autoimmune diseases.

Micronutrient deficiency is increasingly showing up as a major underlying driver

of chronic disease including autoimmune disease.
The immune system is a nutrient hog. It uses micronutrient resources like no other system in the body.
And it needs a vast array of nutrients, including essential fatty acids, essential amino acids, vitamins,
minerals, and plant phytochemicals, to do its work effectively. When the body is low on these nutri-
ents, the first aspect of the immune system that suffers is the regulatory part, the part responsible for
turning off inflammation when the job is done. When we’re deficient in nutrients, our immune system
doesn’t do a good job of regulating itself and tends to get turned on and stay on.

Many of us think that nutrient deficiencies are mainly a problem in developing nations (whereas in
Westernized countries like the United States, our problem is that we have too much food!), but this is
a misconception. The Standard American Diet is definitely energy-rich, but it’s also nutrient-poor: the
types of food that many people eat each day are high in added sugars, refined grains, and industrially
processed oils, but devoid of the vitamins and minerals (and other health-promoting compounds) found
in whole foods. The result is a high prevalence of nutrient deficiency right in our own backyard.

19 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
The Good News
It’s easy to feel that our own health is beyond our control—we blame our genetics or our environment,
we say it runs in our family, our doctors tell us that it’s just bad luck and that no one knows why one
person gets a particular disease while the next one remains healthy.

But in truth, we do have control: our health is almost entirely within our power to
change and improve. And it starts when we make one healthy choice at a time.
Environmental contributors to autoimmune disease can be broadly divided into those that are easy to
control (like diet, sleep, and stress) and those that are more challenging or impossible to control (like
previous infection and some forms of chemical exposure). It’s not possible to change your genetics or
your infection history, but you can change what you eat and make more informed choices about sleep,
activity, and stress. You can remove the diet and lifestyle triggers of your autoimmune disease, heal
your gut and improve your microbiome, fix nutritional deficiencies, give your immune system the
opportunity and resources it needs to regulate itself, provide the opportunity and resources that your
tissues need to heal--all of which leads to decreased disease progression, reduced symptoms and even
disease remission.

The framework that maximizes the potential therapeutic value of healthy foods and lifestyle?

It’s called the Autoimmune Protocol.

Learn More about

gut health with the
Leaky Gut Mini-Course!

LEARN MORE
 Essential Nutrient Deficiency
and Autoimmune Disease

V I TA M I N A 56% of Americans rarely meet the RDA

Deficiency is strongly associated with impaired immunity and susceptibility toinfectious
disease and has been associated with several autoimmune diseases, including alopecia
areata, multiple sclerosis, and autoimmune hepatitis.

V I TA M I N B 6 54% of Americans rarely meet the RDA

Vitamin B6 is converted into the coenzyme form pyridoxal 5 ‘-phosphate (PLP), deficiency
of which has been linked to type 1 diabetes.

V I TA M I N B 9 75% of Americans rarely meet the RDA

Vitamin B9 (folate) deficiency has been associated with cerebral folate deficiency syndrome,
rheumatoid arthritis, Sjogren’s syndrome, celiac disease, Crohn’s disease and ulcerative
colitis.

V I TA M I N B 12 30% of Americans rarely meet the RDA

Vitamin B12 deficiency has been associated with multiple sclerosis, celiac disease, Sjogren’s
syndrome, Crohn’s disease, ulcerative colitis, autoimmune atrophic gastritis, alopecia areata
and type 1 diabetes.

V I TA M I N C 38% of Americans rarely meet the RDA

Deficiency is associated with lichen planus and idiopathic thrombocytopenic purpura.

V I TA M I N D An estimated 75% of Americans are deficient

Vitamin D deficiency is strongly linked to autoimmune disease and has been implicated as
an environmental trigger for systemic lupus erythematosus, type 1 diabetes, autoimmune
interstitial lung disease, multiple sclerosis, rheumatoid arthritis, celiac disease, psoriasis,
and inflammatory bowel disease.

V I TA M I N E 60% of Americans rarely meet the RDA

Vitamin E deficiency has been implicated in psoriasis, vitiligo, alopecia areata, and
rheumatoid arthritis. Vitamin E supplementation reduced inflammation in patients with
rheumatoid arthritis.

C O P P E R 31% of Americans rarely meet the RDA

Deficiency is associated with rheumatoid arthritis and pemphigus vulgaris.

I O D I N E 74% of Americans rarely meet the RDA

Deficiency is associated with Hashimoto’s thyroiditis and Grave’s disease.

21 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 I R O N 39% of Americans rarely meet the RDA
Iron deficiency is a hallmark of autoimmune hemolytic anemia, autoimmune aplastic
anemia, and pernicious anemia. Deficiency is also associated with rheumatoid arthritis,
autoimmune gastritis, systemic lupus erythematosus, Sjogren’s syndrome and celiac
disease.

M A G N E S I U M 68% of Americans rarely meet the RDA

Deficiency is associated with systemic lupus erythematosus.

S E L E N I U M 15% of Americans rarely meet the RDA

Deficiency is associated with Hashimoto’s thyroiditis, Grave’s disease, pemphigus vulgaris
and lichen planus.

Z I N C 73% of Americans rarely meet the RDA

Deficiency is associated with rheumatoid arthritis, multiple sclerosis, pemphigus vulgaris,
Alzheimer’s disease, autoimmune hepatitis, primary biliary cirrhosis, autoimmune thyroid
disease, systemic lupus erythematosus, celiac disease and type 1 diabetes.

D H A & E PA 70% of Americans rarely meet the RDA

Supplementation has been shown to be beneficial in rheumatoid arthritis, Crohn’s disease,
ulcerative colitis, psoriasis, systemic lupus erythematosus, multiple sclerosis,
autoimmune-mediated glomerulonephritis.

P H Y TO C H E M I C A L S No RDA established
Supplementation has been shown to be beneficial in autoimmune thyroiditis, type 1
diabetes, and rheumatoid arthritis.

22 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Infections Linked to Autoimmune Disease
When the immune system is forming antibodies against an infectious organism, there is
a chance that those antibodies will also target a protein in the human body, i.e., antibody
cross-reactivity resulting in autoimmunity (these antibodies are also called autoantibod-
ies). Infection with the following bacteria, viruses and parasites increases lifetime risk of
specific autoimmune diseases. Other associations are highly likely as this is an emerging
field of research.

B O R R E L I A is a spirochete bacteria typically transmitted by lice and ticks. Infection is

associated with chronic Lyme disease, rheumatoid arthritis, sarcoidosis, schizophrenia*
and dementia*.

C H L A MY D O P H I L A P N E U M O N I A E is a bacteria that causes pharyngitis, bronchi-

tis, and atypical pneumonia. Infection is linked to arthritis, myocarditis, Guillain-Barré
syndrome, Alzheimer’s disease*, chronic fatigue syndrome*, chronic obstructive
pulmonary disease*, multiple sclerosis, and Tourette syndrome.

E N T E R O V I R U S are viruses of the gastrointestinal tract that cause a wide range of dis-
eases. They are linked to amyotrophic lateral sclerosis*, chronic fatigue syndrome*, type 1
diabetes, Guillain-Barré syndrome, and schizophrenia*.

G I A R D I A L A M B L I A is a parasite that causes “beaver fever” or “backpacker’s

diarrhea”. Infection is linked to multiple sclerosis, amyotrophic lateral sclerosis*,
Parkinson’s disease*, chronic fatigue syndrome*, arthritis, and uveitis.

H E L I C O B A C T E R P Y L O R I is a bacteria that causes chronic gastritis, stomach ulcers,

and linked to stomach cancer. Infection is associated with immune thrombocytopenia, pso-
riasis, and sarcoidosis.

H E R P E S V I R U S is a virus family causing wide range of illness, such as mononucleosis

and roseola. Cytomegalovirus infection is associated with Guillain-Barré syndrome and
systemic lupus erythematosus. Epstein-Barr infection is associated with dermatomyositis,
systemic lupus erythematosus, rheumatoid arthritis, Sjögren’s syndrome, and multiple
sclerosis. Human herpesvirus 6 infection is associated with multiple sclerosis and chronic
fatigue syndrome*.

* suspected autoimmune disease

23 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 N O R O V I R U S is a virus causing gastroenteritis. Infection is associated with Crohn’s
disease.

PA R V O V I R U S B 19 is a virus that causes a childhood rash called fifth disease and a

form of acute arthritis. Infection is associated with rheumatoid arthritis,
systemic lupus erythematosus and vasculitis.

S T R E P TO C O C C U S is the bacteria that causes strep throat. Infection is

associated with Tourette syndrome.

TO X O P L A S M A G O N D I I is a parasite causing toxoplasmosis. Infection is linked

to Alzheimer’s disease*, Parkinson’s disease*, Tourette syndrome, antiphospholipid
syndrome, systemic sclerosis, and inflammatory bowel diseases.

* suspected autoimmune disease

24 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 THE MOST COMMON
AUTOIMMUNE DISEASES
Wondering if you have an autoimmune disease? Below are the twelve most common autoimmune
diseases along with prevalence and common symptoms.

Note that for many autoimmune diseases, severity of symptoms can vary
dramatically from person to person, and you may only experience one or two
of the possible symptoms.

For example, only a third of adults with celiac disease have gastrointestinal symptoms, and there’s even
something called silent celiac disease in which there are no outward indicators.

SJÖGREN’S SYNDROME:
A systemic autoimmune disorder characterized by dry eyes and dry mouth.
Affects: up to 1 in 29 people
Symptoms: dry cough, dry eyes, dry skin, fatigue, joint stiffness, swollen lymph nodes, vaginal
dryness and possibility of serious complications such as crippling fatigue, chronic pain, major organ
involvement, neuropathies and lymphomas

HASHIMOTO’S THYROIDITIS:
An autoimmune condition in which the thyroid does not make enough hormones for the body’s needs.
Affects: up to 1 in 34 people
Symptoms: dry or rough skin, hair loss, constipation, depression, enlarged thyroid, fatigue, joint stiff-
ness, muscle weakness, puffy eyes, sensitivity to cold, slow heart rate, swelling in extremities, unex-
plained weight gain

CELIAC DISEASE:
An autoimmune condition in which the small intestine is inflamed and damaged in response to eating
gluten, a protein found in wheat, barley, and rye.
Affects: up to 1 in 53 people
Symptoms: abdominal pain, belching, diarrhea, steatorrhea (found-smelling, fatty, pale stools), heart-
burn, indigestion, nausea, vomiting, cramping, flatulence, joint pain, loss of bone density (osteopenia
or osteoporosis), fatigue, malnutrition (anemia), delayed puberty, slow growth in children, itching, skin
rash, weight loss, chronic fatigue, chronic migraine, peripheral neuropathy (tingling, numbness or pain
in hands or feet), unexplained liver damage, unexplained infertility, depression and anxiety, eczema.

25 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ALOPECIA AREATA:
Sudden hair loss that starts with one or more circular bald patches that may overlap.
Affects: up to 1 in 59 people
Symptoms: hair loss, anxiety, itching, small dents in nails

PSORIASIS:
A condition in which skin cells build up and form scales and itchy, dry patches.
Affects: up to 1 in 65 people
Symptoms: rashes, dry skin, skin fissures, flaky skin, peeling skin, small bumps on skin,
thickening skin, skin redness, joint pain, depression, inflamed tendons, joint stiffness, itching, small
dents in nails

T YPE 1 DIABETES:
A chronic condition in which the pancreas produces little or no insulin.
Affects: up to 1 in 106 people
Symptoms: excessive thirst, fatigue, excessive hunger, excessive sweating, nausea or vomiting,
excessive urination (bedwetting in children), blurred vision, elevated heart rate, headache, fatigue,
unexplained weight loss

RHEUMATOID ARTHRITIS:
A chronic inflammatory disorder affecting many joints, including those in the hands and feet.
Affects: up to 1 in 123 people
Symptoms: joint pain, back pain, joint stiffness, joint swelling, joint tenderness, joint weakness, mus-
cle pain, fatigue, anemia, malaise, skin redness or lumps, swelling in fingers, dry mouth, physical defor-
mity, sensation of pins and needles

POLYMYALGIA RHEUMATICA:
An inflammatory disorder causing muscle pain and stiffness around the shoulders and hips.
Affects: up to 1 in 135 people
Symptoms: shoulder pain, neck pain, pelvic girdle pain, joint stiffness, joint tenderness, fatigue

GRAVE’S DISEASE:
An autoimmune disorder that results in the overproduction of thyroid hormones.
Affects: up to 1 in 160 people
Symptoms: excess sweating, fatigue, heat intolerance, high blood pressure, elevated heart rate,
irregular heart rate, heart palpitations, anxiety, nervousness, abnormal protrusion of eyes, puffy eyes,
absence of menstruation, diarrhea, enlarged thyroid, hair loss, hand tremor, insomnia, irritability,
muscle weakness, puffy skin changes on the shin, unexplained weight loss

26 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MULTIPLE SCLEROSIS:
A disease in which the immune system eats away at the protective covering of nerves.
Affects: up to 1 in 279 people
Symptoms: Pain in the back or eyes, tremor, muscle cramping, difficulty walking, inability to rapidly
change motions, involuntary movements, muscle paralysis, muscle rigidity, muscle weakness, problems
with coordination, stiff muscles, clumsiness, muscle spasms, overactive reflexes, fatigue, dizziness, heat
intolerance, poor balance, vertigo, sensations of pins and needles, abnormality of taste, reduced sensa-
tion of touch, uncomfortable tingling and burning, excessive urination at night, leaking of urine, per-
sistent urge to urinate, urinary retention, blurred vision, double vision, vision loss, erectile dysfunction,
sexual dysfunction, anxiety, mood swings, difficulty speaking, slurred speech, constipation, depression,
difficulty swallowing, difficulty thinking and understanding, headache, heavy legs, numbness of face,
rapid involuntary eye movement, sleep deprivation, tongue numbness or weakness, difficulty raising
the foot

ULCERATIVE COLITIS:
A disease that causes inflammation and sores (ulcers) in the lining of the large intestine
Affects: up to 1 in 264 people
Symptoms: abdominal pain, rectal pain, bloating, cramping, blood in stool, constipation, diarrhea,
inability to empty bowels, leaking of stool, urgent need to defecate, loss of appetite, joint pain, anemia,
fatigue, fever, unexplained weight loss

CROHN’S DISEASE:
A type of inflammatory bowel disease (IBD) that may affect any part of the gastrointestinal tract.
Affects: up to 1 in 444 people
Symptoms: abdominal pain, rectal pain, bloating, cramping blood in stool, bowel obstruction, diarrhea,
nausea, vomiting, flatulence, anal fissure, loss of appetite, mouth ulcer, joint pain, fatigue, fever,
depression, slow growth in children, unexplained weight loss

27 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 COMPREHENSIVE LIST OF
AUTOIMMUNE DISEASES
The following is the up-to-date list of confirmed and suspected autoimmune diseases compiled by the
American Autoimmune Related Diseases Association (aarda.org):

Achalasia Chagas disease

ºº ºº
Addison’s disease Chronic inflammatory demyelinating
ºº ºº polyneuropathy (CIDP)
Adult Still’s disease
ºº Chronic recurrent multifocalosteomy
ºº
Agammaglobulinemia
ºº elitis (CRMO)
Alopecia areata
ºº Churg-Strauss Syndrome (CSS) or
ºº
Amyloidosis
ºº Eosinophilic Granulomatosis (EGPA)
Ankylosing spondylitis
ºº Cicatricial pemphigoid
Anti-GBM/Anti-TBM nephritis ºº
ºº Cogan’s syndrome
Antiphospholipid syndrome ºº
ºº Cold agglutinin disease
Autoimmune angioedema ºº
ºº Congenital heart block
Autoimmune dysautonomia ºº
ºº Coxsackie myocarditis
Autoimmune encephalomyelitis ºº
ºº CREST syndrome
Autoimmune hepatitis ºº
ºº Crohn’s disease
Autoimmune inner ear disease (AIED) ºº
ºº Dermatitis herpetiformis
Autoimmune myocarditis ºº
ºº Dermatomyositis
Autoimmune oophoritis ºº
ºº Devic’s disease (neuromyelitis optica)
Autoimmune orchitis ºº
ºº Discoid lupus
Autoimmune pancreatitis ºº
ºº Dressler’s syndrome
Autoimmune retinopathy ºº
ºº Endometriosis
Autoimmune urticaria ºº
ºº Eosinophilic esophagitis (EoE)
Axonal & neuronal neuropathy (AMAN) ºº
ºº Eosinophilic fasciitis
Baló disease ºº
ºº Erythema nodosum
Behcet’s disease ºº
ºº Essential mixed cryoglobulinemia
Benign mucosal pemphigoid ºº
ºº Evans syndrome
Bullous pemphigoid ºº
ºº Fibromyalgia
Castleman disease (CD) ºº
ºº Fibrosing alveolitis
Celiac disease ºº
ºº

28 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Giant cell arteritis (temporal arteritis) Microscopic polyangiitis (MPA)
ºº ºº
Giant cell myocarditis Mixed connective tissue disease
ºº ºº (MCTD)
Glomerulonephritis
ºº Mooren’s ulcer
ºº
Goodpasture’s syndrome
ºº
Mucha-Habermann disease
ºº
Granulomatosis with Polyangiitis
ºº
Multifocal Motor Neuropathy (MMN) or
ºº
Graves’ disease
ºº MMNCB
Guillain-Barre syndrome
ºº Multiple sclerosis
ºº
Hashimoto’s thyroiditis
ºº
Myasthenia gravis
ºº
Hemolytic anemia
ºº
Myositis
ºº
Henoch-Schonlein purpura (HSP)
ºº
Narcolepsy
ºº
Herpes gestationis or pemphigoid
ºº
Neonatal Lupus
gestationis (PG)
ºº
Neuromyelitis optica
ºº
Hidradenitis Suppurativa (HS)
ºº
(Acne Inversa) Neutropenia
ºº
Hypogammalglobulinemia Ocular cicatricial pemphigoid
ºº ºº
IgA Nephropathy Optic neuritis
ºº ºº
IgG4-related sclerosing disease Palindromic rheumatism (PR)
ºº ºº
Immune thrombocytopenic purpura PANDAS
ºº (ITP)
ºº
Paraneoplastic cerebellar degeneration
Inclusion body myositis (IBM)
ºº (PCD)
ºº
Interstitial cystitis (IC) Paroxysmal nocturnal hemoglobinuria
ºº ºº (PNH)
Juvenile arthritis
ºº Parry Romberg syndrome
ºº
Juvenile diabetes (Type 1 diabetes)
ºº
Pars planitis (peripheral uveitis)
ºº
Juvenile myositis (JM)
ºº
Parsonage-Turner syndrome
ºº
Kawasaki disease
ºº
Pemphigus
ºº
Lambert-Eaton syndrome
ºº
Peripheral neuropathy
ºº
Leukocytoclastic vasculitis
ºº
Perivenous encephalomyelitis
ºº
Lichen planus
ºº
Pernicious anemia (PA)
ºº
Lichen sclerosus
ºº
POEMS syndrome
ºº
Ligneous conjunctivitis
ºº
Polyarteritis nodosa
ºº
Linear IgA disease (LAD)
ºº
Polyglandular syndromes type I, II,
ºº
Lupus
ºº III
Lyme disease chronic
ºº Polymyalgia rheumatica
ºº
Meniere’s disease
ºº
29 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 Polymyositis Scleritis
ºº ºº
Postmyocardial infarction syndrome Scleroderma
ºº ºº
Postpericardiotomy syndrome Sjögren’s syndrome
ºº ºº
Primary biliary cirrhosis Sperm & testicular autoimmunity
ºº ºº
Primary sclerosing cholangitis Stiff person syndrome (SPS)
ºº ºº
Progesterone dermatitis Subacute bacterial endocarditis (SBE)
ºº ºº
Psoriasis Susac’s syndrome
ºº ºº
Psoriatic arthritis Sympathetic ophthalmia (SO)
ºº ºº
Pure red cell aplasia (PRCA) Takayasu’s arteritis
ºº ºº
Pyoderma gangrenosum Temporal arteritis/Giant cell arteritis
ºº ºº
Raynaud’s phenomenon Thrombocytopenic purpura (TTP)
ºº ºº
Reactive Arthritis Tolosa-Hunt syndrome (THS)
ºº ºº
Reflex sympathetic dystrophy Transverse myelitis
ºº ºº
Relapsing polychondritis Type 1 diabetes
ºº ºº
Restless legs syndrome (RLS) Ulcerative colitis (UC)
ºº ºº
Retroperitoneal fibrosis Undifferentiated connective tissue
ºº ºº disease (UCTD)
Rheumatic fever
ºº Uveitis
ºº
Rheumatoid arthritis
ºº
Vasculitis
ºº
Sarcoidosis
ºº
Vitiligo
ºº
Schmidt syndrome
ºº

30 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Go deeper into
the Science behind the
Autoimmune Protocol with
The Paleo Approach

LEARN MORE

The Paleo Approach

The Paleo Approach is the New York Times bestselling complete guide to using diet and lifestyle to
manage autoimmune disease and other chronic illnesses. With over 400 pages of scientific explanations
of the why’s, what’s, and how’s behind diet and lifestyle recommendations to help regulate the immune
system and provide the body with the opportunity to heal. This encyclopedic resource also contains tons
of practical information including tips for transitions, working with your doctor, medical test and treat-
ments that might be helpful, troubleshooting, and when and how to reintroduce foods. This book goes into
scientific detail, while keeping explanations accessible and fun to read, and includes over 1200 scientific
references. This is the book for people who want to understand the contemporary science behind how the
food we eat as well as how we live our daily lives together impact our bodies to either promote health or
facilitate disease.

31 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 PA R T T W O

The Autoimmune Protocol

32 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 AN INTRODUCTION TO THE
AUTOIMMUNE PROTOCOL
The medical establishment offers no cure for autoimmune diseases. Treatment, or management, varies
with the disease. Generally, hormone replacement is the protocol for diseases that result in a hormone
deficiency (as in the case of hypothyroidism or type 1 diabetes). Corticosteroids are often used to
suppress the immune system, generally with many unwanted side effects.

Stronger immunosuppressant drugs (including disease-modifying antirheumatic drugs, or DMARDs)

are available for very ill patients but come with greater risks, especially for long-term use, such as
increased susceptibility to infection and risk of developing cancer. Medication for pain and other
symptom management are also prescribed when appropriate. Although typical treatment does not
currently include diet and lifestyle modifications, the evidence is accumulating for their inclusion.

In fact, many people can manage and even reverse their autoimmune diseases
just by making changes in diet and lifestyle.

Good health comes from a collection of small changes, each one contributing its own tiny bit to an
overall big improvement. And, at its core, that’s what the Autoimmune Protocol is: a framework for
informing your day-to-day diet and lifestyle choices to truly support better health.

What is the Autoimmune Protocol?

The Autoimmune Protocol, abbreviated AIP, is a complementary approach to chronic disease manage-
ment focused on providing the body with the nutritional resources required for immune regulation,
gut health, hormone regulation and tissue healing while removing inflammatory stimuli from both
diet and lifestyle. The AIP diet provides balanced and complete nutrition while avoiding processed and
refined foods and empty calories. The AIP lifestyle encourages sufficient sleep, stress management and
activity as these are important immune modulators.

Foods can be viewed as having two kinds of constituents within them: those that
promote health (like nutrients!) and those that undermine health (like inflammatory
compounds).
While there are constituents that neither promote nor undermine health, they are not used to
evaluate the merit of an individual food.) Some foods are obvious wins for a health-promoting diet
because they have tons of beneficial constituents and very few or no constituents that undermine

33 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 health—good examples of these superfoods are organ meats, seafood, and most vegetables. Other foods
are obvious fails because they have a relative lack of health-promoting constituents and are rife with
problematic compounds—good examples are gluten-containing grains, peanuts, and most soy products.
But many foods fall into the amorphous world of gray in between these two extremes. Tomatoes, for
example, have some exciting nutrients, but they also contain several compounds that are so effective
at stimulating the immune system that they have been investigated for use in vaccines as adjuvants
(the chemicals in vaccines that enhance your immune response to whatever you’re getting immunized
against).

The biggest difference between the Autoimmune Protocol and other dietary
templates that take a nutrients-first approach while considering inflammation
triggers is where we draw the line between “yes” foods and “no” foods in order to get
more health-promoting compounds and fewer detrimental compounds in our diet.

Those who are typically quite healthy can tolerate less-optimal foods than those who aren’t. You can
think of the Autoimmune Protocol as a pickier version of other evidence-based dietary templates; it
accepts only those foods that are clear winners.

As such, the Autoimmune Protocol places greater emphasis on the most nutrient-dense foods in our food
supply, including organ meat, seafood, and vegetables. The Autoimmune Protocol eliminates foods
endorsed by other healthy diets that have compounds that may stimulate the immune system or harm
the gut environment, including nightshades (like tomatoes and peppers), eggs, nuts, seeds, and alcohol.
The goal of the Autoimmune Protocol is to flood the body with nutrients while simultaneously avoiding
any food that might be contributing to disease (or at the very least interfering with our efforts to heal).

The AIP is an elimination diet strategy, cutting out the foods that are most likely to be holding back our
health. After a period of time, many of the excluded foods, especially those that have nutritional merit
despite also containing some (but not too much) potentially detrimental compounds, can be reintro-

34 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 duced. The AIP is not a life sentence, but rather a toolbox full of strategies for understanding how your
body reacts to foods, lifestyle and your environment and methodologies for healing given your individu-
al health challenges.

The AIP is also a holistic approach to health, including not only a dietary framework but
also a focus on lifestyle factors known to be important modulators of immune function,
gut health, and hormone health.

This includes a strong focus on getting adequate sleep,

managing stress, and living an active lifestyle while Talk to Your Doctor
avoiding overtraining. These three lifestyle factors are
each essential for gut health because they directly
influence the gut microbiome (getting enough sleep,
keeping stress levels in check, and being active are
all essential for a healthy and diverse gut microbial
community in addition to supporting the growth of key
probiotic strains). Chronic stress and overtraining also
increase intestinal permeability. Sleep, stress and activ-
ity are all essential hormone modulators; for As is always the case with chronic
example, insulin sensitivity is more strongly disease, consult with your physician
influenced by these lifestyle factors than it is by diet. before beginning this or any other
Most importantly, immune function is directly tied regimen, or altering medications or
to lifestyle. Inflammation is triggered by getting supplements.
inadequate sleep, feeling stressed, being sedentary,
and overtraining. Furthermore, the regulatory
aspects of the immune system are most active while we’re sleeping, and sleep quality is linked to stress.
Additionally, there’s emerging evidence that a strong sense of connection and community as well as
spending time in natural environments also contribute to a healthier immune system.

Drawing on insights gleaned from more than 1,200 scientific studies, the AIP is now supported by clinical
trial evidence. In a recent study, fifteen patients with active inflammatory bowel disease were placed on
the Autoimmune Protocol by transitioning gradually over 6 weeks, followed by a 5-week maintenance
phase. Patients were closely monitored and given access to health coaching. They were also given two
books The Paleo Approach by Dr. Sarah Ballantyne, PhD (which remains the definitive AIP guidebook) and
The Autoimmune Wellness Handbook by Mickey Trescott, NTP and Angie Alt, NTC, CHC, as resources
for following the protocol. Clinical remission was achieved by week 6 (yes, just by completing the tran-
sition to the AIP) in eleven of the fifteen participants (73%!!), and they stayed in remission throughout
the 5-week maintenance phase of the study. All patients, including those whom didn’t achieve clinical
remission, experienced quantifiable improvement in disease activity over the entire course of the study.

35 THE AUTOIMMUNE PROTOCOL

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 The clinical research studies performed using the Wahls
Protocol in multiple sclerosis provide additional
validation for the Autoimmune Protocol. While there
are a handful of foods included on the Wahls Protocol
(most notably nightshades) that are excluded on the
Autoimmune Protocol, the two protocols are remarkably
similar despite the different philosophies that went into
their formulation. The Wahls Protocol framework was
developed with mitochondrial health as its primary goal
whereas the Autoimmune Protocol framework was devel-
oped with immune regulation and gut health as its pri-
mary goals. It so happens that the nutrients required for
mitochondrial health are nearly identical to those
required for immune and gut health, hence the high
degree of overlap between both approaches.

A growing number of clinicians, especially functional and integrative medicine specialists, are
recommending the AIP to their patients, adding to the large body of anecdotal evidence supporting
the efficacy of the Autoimmune Protocol. Most exciting, there is ongoing clinical research to quantify
improvement in specific autoimmune diseases with a short-term intervention with the AIP, including
research in Hashimoto’s thyroiditis. As the results from more and more clinical trials are published,
there is increasing attention being paid to diet and lifestyle, not as a complementary approach to
autoimmune disease management, but as a first-line course of treatment.

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by Dr. Sarah Ballantyne, PhD
 How Does The Autoimmune Protocol Work?
The Autoimmune Protocol works by addressing four key areas known to be important contributors
to chronic and autoimmune diseases.

NUTRIENT DENSIT Y.
The immune system (and indeed every system in the body) requires an array of
vitamins, minerals, antioxidants, essential fatty acids, and amino acids to
function normally. Micronutrient deficiencies and imbalances are key players
in the development and progression of autoimmune disease. Focusing on con-
suming the most nutrient-dense foods available enables a synergistic surplus
of micronutrients to correct both deficiencies and imbalances, thus supporting
regulation of the immune system, hormone systems, detoxification systems, and neurotransmitter
production. A nutrient-dense diet further provides the building blocks that the body needs to heal
damaged tissues.

GUT HEALTH.
Gut dysbiosis and leaky gut are key facilitators in the development of
autoimmune disease. The foods recommended on the Autoimmune Protocol
support the growth of healthy levels and a healthy variety of gut microor-
ganisms. Foods that irritate or damage the lining of the gut are avoided, while
foods that help restore gut barrier function and promote healing are endorsed.
Lifestyle factors that strongly influence gut barrier health as well as gut microbial composition are also
addressed on the Autoimmune Protocol. Because of the link between gut health and immune function,
restoring a healthy gut barrier and microbiome are necessary precursors to healing.

HORMONE REGUL ATION.

What we eat, when we eat, and how much we eat affect a variety of hormones
that interact with the immune system. When dietary factors (like eating too
much sugar or grazing rather than eating larger meals spaced farther apart)
dysregulate these hormones, the immune system is directly affected (typically
stimulated). The Autoimmune Protocol diet is designed to promote regulation
of these hormones, thereby regulating the immune system by proxy. These and
other essential hormones that impact the immune system are also profoundly affected by how much
sleep we get, how much time we spend outside, how much and what kinds of activity we get, and how
well we reduce and manage stress.

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by Dr. Sarah Ballantyne, PhD
 IMMUNE SYSTEM REGUL ATION.
Immune regulation is achieved by restoring a healthy diversity and healthy
amounts of gut microorganisms, restoring the barrier function of the gut,
providing sufficient amounts of the micronutrients required for the immune
system to function normally, and regulating the key hormones that in turn
regulate the immune system. The Autoimmune Protocol diet and lifestyle provide both the resources
and the opportunity for immune regulation. Immune regulation combined with tissue healing account
for reductions in symptoms.

AIP for Other Chronic Illnesses?

Inflammation is a factor in all chronic illnesses, and this is
one area where the foods we eat can make a huge difference.
In some cases, an immune system that isn’t regulating itself
properly directly causes the illness; in others, inflammation is
merely an element of the illness or a contributor to how the
illness came about—but it is always a player and a problem. What this means is that
reducing inflammation and giving the immune system the resources it needs, as well as
the opportunity to regulate itself, can help in every single chronic illness, not just
autoimmune disease. This is important because inflammation is strongly influenced by
what we eat, how well we sleep, how stressed we are, and how active we are. And this is
why chronic illness can respond so positively to changes in diet and lifestyle.

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by Dr. Sarah Ballantyne, PhD
 THE SCIENCE BEHIND
THE AIP
The Paleo Approach by Dr. Sarah Ballantyne, PhD provides detailed scientific rationale including more
than 1,200 citations for every aspect of the Autoimmune Protocol, including why some foods need to
be avoided and why it’s important to eat more of others, and why it’s important to get more sleep,
manage stress, and get the right amounts of the right kinds of activity. And for those that thrive in a
multimedia learning environment, Dr. Sarah has created The AIP Lecture Series, a 6-week self-directed
intensive online course that will teach you the scientific foundation for the diet and lifestyle tenets of
the Autoimmune Protocol, plus provide tons of tips and strategies for implementation, refinement and
troubleshooting!

Though it’s not essential to understand the science behind the Autoimmune Protocol recommendations
in order to implement and benefit from them, many people find motivation in the knowledge that these
recommendations have a firm scientific foundation. Here are some of the highlights:

Nutrient Density
ºº Autoimmune diseases have been linked to dietary insufficiencies of a staggering
A nutrient-poor diet is one of the biggest risk factors for autoimmune disease.

number of vitamins and minerals, as well as to insufficiencies in antioxidants,

fiber, and essential fatty acids.

ºº antioxidants), plus essential fatty acids and amino acids, to function normally.
The immune system requires micronutrients (water-soluble and fat-soluble vitamins, minerals, and

ºº system regulation, including vitamins A and D, and zinc.

Some of the nutrients that we’re most likely to be deficient in are the most important for immune

ºº caveat that it’s important to limit saturated fat to no more than 15% of total calories), and it is essen-
Eating fat is good for you. The healthiest fats are saturated and monounsaturated fats (with the

tial to consume a balanced ratio of omega-6 to omega-3 polyunsaturated fatty acids (ideally between
1:1 and 4:1).

ºº on quality meats, seafood, vegetables, and fruits is the healthiest and most effective way to ensure
Eating fat is necessary for the absorption of fat-soluble vitamins. Eating a nutrient-dense diet based

that your body is getting all the nutrients it needs for optimal health.

ºº have less of an impact on your well-being, and help regulate important hormones and
Increasing nutrient density can increase your resilience to stress, meaning that stressors in your life

neurotransmitters.

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by Dr. Sarah Ballantyne, PhD
 Gut Health
ºº
A leaky gut is necessary for autoimmune disease to develop.

ºº agglutinins, such as wheat germ agglutinin—cause increased intestinal

A variety of proteins in grains—including prolamins, such as gluten, and

permeability (gut leakiness) and feed bacterial overgrowth in the gut.

ºº products cause inflammation in the gut and feed bacterial overgrowth in the gut.
Digestive enzyme inhibitors in grains, legumes, nuts, seeds, and dairy

ºº may increase intestinal inflammation and gut dysbiosis.

A high dietary intake of phytates or phytic acid—found in grains, legumes, nuts, and seeds—

ºº intestinal permeability. Other saponins found in legumes may also be problematic.

Types of saponins called glycoalkaloids, found in vegetables of the nightshade family, cause increased

ºº overgrowth and dysbiosis.

Alcohol consumption causes increased intestinal permeability, damages the gut, and feeds bacterial

ºº and damage to the liver. It’s best to aim for 10 to 25 grams daily.
Excessive fructose intake (more than 40 grams per day) may cause increased intestinal permeability

ºº permeability.
All sugar substitutes have negative health effects, and many of them cause increased intestinal

ºº gut dysbiosis.
Too much omega-6 fatty acids cause gut dysbiosis. Increasing omega-3 fatty acid intake helps correct

ºº calories from saturated fats.

Too much saturated fat also skews gut bacteria towards unfavorable strains. Aim for 10% to 15% total

ºº supports a healthy variety and amount of probiotic gut organisms. Aim for 8+ servings daily.
A diet rich in vegetables, including plenty of nonstarchy vegetables and some starchy vegetables,

ºº
Probiotic-rich foods support a healthy gut microbiome.

ºº restore gut barrier function.

Foods rich in vitamin A, vitamin D, vitamin K2, and the amino acids glutamine and glycine can help

ºº
The medium-chain triglycerides in coconut oil may help restore gut barrier function.

ºº
Reducing and managing stress is critical for gut barrier health and gut microbiome health.

Living an active lifestyle (but avoiding overtraining) supports a healthy, diverse gut microbiome.
ºº

Hormone Regulation
ºº
High-carbohydrate diets cause insulin resistance and leptin resistance.

ºº get enough fiber and phytochemicals on a low-carb diet), but avoiding a high-
Following a low-carbohydrate diet is not optimal (it’s nearly impossible to

carbohydrate diet is.

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by Dr. Sarah Ballantyne, PhD
 ºº is important. This approach helps regulate insulin and insulin sensitivity as well as leptin and leptin
Regulating blood glucose levels and insulin release by eating low- to moderate-glycemic-load foods

sensitivity.

ºº after eating. Dietary fructose should be maintained in the 10- to 20-grams-per-day range.
Fructose causes insulin resistance and leptin resistance. Fructose also doesn’t suppress ghrelin levels

ºº contain protein, fat, and low- to moderate-glycemic-load vegetables and fruits and minimizing
Hunger hormones are intricately linked to the immune system. Eating large, balanced meals that

snacking is the best way to regulate hunger hormones.

ºº immune system.
Cortisol levels may rise as a result of skipping meals or intermittent fasting and stimulate the

ºº ghrelin levels and may regulate peristalsis by increasing gastrointestinal melatonin production.
Dietary fiber, especially insoluble fiber, from whole-food sources such as vegetables helps regulate

ºº adequate sleep help regulate critical hormones.

Reducing and managing stress, getting plenty of low- and moderate-intensity activity, and getting

Immune Health
ºº optimally. Eating a nutrient-dense diet is the best way to supply the immune
The immune system requires a tremendous amount of nutrients to function

system with those nutrients.

ºº agglutinins, such as wheat germ agglutinin—stimulate the immune system.

A variety of proteins in grains—including prolamins, such as gluten, and

ºº
Gluten may be an important trigger in all autoimmune diseases.

ºº
Digestive enzyme inhibitors in grains, legumes, nuts, seeds, and dairy products cause inflammation.

Types of saponins called glycoalkaloids, found in vegetables of the nightshade family, significantly
ºº stimulate the immune system. Other saponins found in legumes may also be problematic.

ºº
Alcohol consumption stimulates inflammation.

ºº which then stimulate the immune system.

Proteins found in egg whites act as carrier molecules for bacterial proteins to cross the gut barrier,

ºº
Excessive fructose intake (more than 40 grams per day) causes inflammation.

ºº intake helps reduce inflammation and modulate the immune system. Moderate consumption of
Eating too much omega-6 fatty acids causes inflammation, whereas increasing omega-3 fatty acid

monounsaturated fats and saturated fats is healthy.

ºº
Reducing and managing stress and getting plenty of sleep are critical for normal immune function.

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by Dr. Sarah Ballantyne, PhD
 A NUTRIENTS-FIRST
APPROACH
Nutrient sufficiency, meaning that you consume an ample amount of all the nutrients your body needs,
is arguably the most important quality that any dietary approach can have. Every cell, tissue, organ,
and system in the human body needs specific amounts of specific nutrients in order to function
efficiently and effectively. Nutrients are used not only in the formation of the components of our
bodies but also in the millions of chemical reactions that occur in our bodies in every moment.

We are made of nutrients and our bodies need them to do even basic things like
breathing. Every tiny detail of every function of every part of the human body
requires nutrients, and it isn’t just macronutrients—protein, fat, and carbohydrates—
that supply the energy that fuels the complex functions of life.

Micronutrients—vitamins, minerals, plant phytochemicals, and other compounds—are necessary

resources that get used up, too, and our micronutrient stores must be continuously topped up from the
foods we eat. Being even slightly deficient in a single essential nutrient can have negative consequenc-
es for our health.

Many micronutrients are immune modulators, meaning that sufficient amounts of these substances
are required to regulate the immune system. Although epidemiological studies reveal a correlation
between dietary intake of specific nutrients and increased risk of autoimmune disease, these studies
are mostly designed to direct future research rather than
to insinuate causality. In truth, in most cases, we don’t
know if nutritional deficiency is a precursor to autoim-
mune disease or if nutritional deficiency is a result of
autoimmune disease. Dietary insufficiency or malabsorp-
tion issues contribute to the immune system becoming
overstimulated in autoimmune disease. However, the
need for many micronutrients also increases when there
is inflammation. It could be that those with autoimmune
disease become deficient because their bodies need more
of these vitamins, minerals, and antioxidants to help
control inflammation when their immune systems go into
overdrive. Either way, there is a need for increased intake
of these important nutrients to help control inflamma-
tion, regulate the immune system, and heal the body.

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by Dr. Sarah Ballantyne, PhD
 Unfortunately, getting all of our required nutrients from food is easier said than done. Many of the
staple foods of the typical American diet have very little nutritional value. Even worse, the more a food
is refined and processed and manufactured, the more the nutrients inherent to the raw ingredients are
leached out, removed, or degraded. Processed foods, refined foods, fast food, and junk food all contribute
next to no nutrients to our diets (plus, they’re often problematic for our health in other ways). But even
foods that many people think are healthy, like whole grains and low-fat dairy, are pretty weak when it
comes to essential nutrients. And every time a nutritionally weak food displaces a nutritional power-
house, the overall nutritional value of the diet suffers.

Even following a healthy dietary template, such as the standard Paleo diet, as defined in the last
decade of books and websites, is not a guarantee that you’re getting all the micronutrients you need to
be healthy. And while the foods endorsed by the Paleo diet represent the most nutrient-dense foods
in our food supply, reaching micronutrient sufficiency still requires commitment. In fact, analyses of
typical Paleo food choices reveal that biotin (abundant in liver and root vegetables), calcium (abundant
in its most bioavailable form [meaning that our bodies can easily digest and use it] in dark leafy greens
like kale, as well as in whole fish like sardines), and chromium (abundant in dark leafy greens, oysters,
and liver) are commonly deficient on the Paleo diet. While the Paleo diet far outstrips other approaches
in terms of micronutrient sufficiency, if you just stick to the stereotypical meat, veggies, and coconut oil,
you may miss out on important nutrients for optimal health.

Track Your Micros

How do you know if you’re getting all of the micronutrients your body
needs? Instead of tracking your macros, track your micros! Apps like
Cron-o-meter can help you easily see if you’re meeting the RDA of
essential vitamins and minerals, eating enough fiber, and getting enough
omega-3 fats. Try keeping a food journal for a few days to identify if there
are any nutrients you’re routinely falling short on, then figure out what
foods you can add to your diet to better meet your nutritional needs.

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by Dr. Sarah Ballantyne, PhD
 Becoming a Nutrivore
Generally, a nutrients-first approach to eating, sometimes
termed being a nutrivore, focuses on micronutrients. Once
we’re getting all of the essential amino acids, essential
fatty acids, vitamins, minerals, and plant phytochemicals
that our bodies need to thrive, it’s nearly impossible not to
be consuming sufficient macronutrients.

Micronutrients can be categorized as essential and

nonessential. Essential means that you’ll die without
them. Nonessential means that you’ll go on living without
them, though you may not be particularly healthy—
and indeed, many micronutrients that are considered
nonessential are known to improve health. Often,
micronutrients are called nonessential simply because
we don’t really understand exactly what it does in our bodies to support health—we just know that
when we consume more of it, our risk of disease decreases. This is the case for most phytochemicals
(like polyphenols) and many vitaminlike compounds (like coenzyme Q10). There are thousands of plant
phytochemicals, and our understanding of their roles in health is so rudimentary that the most we can
typically say about them is that they have antioxidant activity (that is, they help prevent damage to
molecules in our body from oxidation). Yet we know that the more plant phytochemicals in your diet,
the lower your risk of chronic disease. When you think about it in these terms, it’s easy to realize that
even non-essential nutrients are pretty darned important.

The term nutrient density refers to the concentration of micronutrients (mainly vitamins
and minerals, but the term micronutrients also encompasses phytochemicals, essential
fatty acids and essential amino acids) per calorie of food.

Nutrient-dense foods supply a wide range of vitamins and minerals (or alternatively, high levels of a
specific, important vitamin or mineral) relative to the calories they contain, whereas low nutrient
density foods supply lots of energy without much in the way of additional nutrition. Thus, a nutri-
ents-first approach is practically achieved by consuming more nutrient-dense foods.

When we consider the foods richest in essential micronutrients, certain foods come up again and again
as powerhouses of nutrition, especially liver and other organ meat, seafood (especially shellfish, but also
fatty fish), and vegetables of all kinds, but notably leafy greens, vegetables from the cruciferous family
(which includes cabbage, broccoli, and kale) and mushrooms. One of the best things you can do to ensure
that your diet is abounding with micronutrients is to eat these foods liberally.

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by Dr. Sarah Ballantyne, PhD
 #THREEQUARTERSVEGGIES
Out of all the foods we could potentially eat, vegetables and fruit are some of the only items not mired
in controversy: virtually every health authority agrees they should have a place at the table (literal-
ly!). In fact, the greatest common denominator among all diets that have a scientific support for their
health-promoting claims is high-vegetable intake. This goes for the Autoimmune Protocol, the Paleo
diet, the Mediterranean diet, plant-based diets, and indigenous diets from around the world. The body of
evidence supporting high intakes of fresh, fibrous, low-energy-density plant foods is truly staggering.

Across the globe, “Blue Zone” areas (which boast a high concentration of centenarians, and are frequent-
ly studied for longevity clues) are characterized first and foremost by their emphasis on vegetables.
The Okinawans consume a famously vegetable-rich diet that includes mineral-rich gourds, bittermel-
on, local herbs and greens, and sweet potatoes. In Costa Rica, residents of the Nicoya Peninsula region
(another longevity hotspot) consume abundant garden vegetables, squash, and tropical fruit (especially
mangoes, papaya, and oranges). People living on the Greek island of Ikaria eat diets rich in fresh, organic
produce and herbs (often grown and picked from their family gardens). The veggie-abundant,
high-micronutrient pattern continues for other centenarian-filled areas like Sardinia, Italy; Acciaroli,
Italy; and Loma Linda, California. (Although Blue Zone diets are often described as plant-based, we
should keep in mind that none of them are vegan, and only one community—the Seventh-Day
Adventists of Loma Linda—is vegetarian.)

High vegetable intake is also a hallmark of hunter-gatherer

diets. Even the Inuit go to great lengths to collect nutrient-
dense plant foods that provide a wide spectrum of micronutri-
ents, prebiotics, and probiotics not available from meat
and fish (including chlorophyll-rich seaweeds, berries, mosses,
wild leafy greens, tubers, and the partially digested stomach
contents of animals).

Of course, the value of vegetables has been confirmed in more

than just studies of homogenous populations (Blue Zone
residents also partake in other health-promoting diet and
lifestyle practices, which makes it hard to tease out the effect
of vegetables alone). Study after study shows that higher
vegetable consumption (at least five to eight servings a day)
reduces the risk of disease, everything from diabetes to
osteoporosis to diseases of the gastrointestinal tract to
cardiovascular disease to autoimmune diseases to cancer.

THE AUTOIMMUNE PROTOCOL

45 by Dr. Sarah Ballantyne, PhD 45
 T H E R E A R E T H R E E L I K E LY R E A S O N S :

ºº the most absorbable form of calcium.

First, vegetables tend to be rich in very important vitamins and minerals, including

ºº microorganisms.
Second, vegetables contain plenty of fiber to support a healthy diversity of gut

ºº with known antioxidant, anti-inflammatory, and other health-promoting properties.

Third, vegetables are rich in thousands of different beneficial plant phytochemicals,

All of these components add up to serious benefits for people who include abundant
vegetables in their diets.

Different types of vegetables and fruits yield different nutrients. This is why variety is so important!
The pigments in different fruits and vegetables are phytochemicals, which is why “eating the rainbow” is
important for ensuring that we consume a wide variety of these beneficial compounds. For example, the
vegetables richest in carotenoids (like α and β-carotene) include anything red, orange, yellow, or dark
green, which includes carrots, beets, squash, sweet potatoes, kale, spinach, collard greens, and broccoli.
Red vegetables, like beets, radicchio and radishes, are also rich in lycopene and anthocyanins. Anthocya-
nins can also be found in vegetables with blue and purple colors, as can anthocyanidins, including purple
varieties of cauliflower, kale, carrots and purple sweet potatoes. Orange and yellow vegetables also
rich in β-cryptoxanthin. Yellow vegetables are additionally rich in xanthophylls. Green veggies provide
chlorophyll, glucosinolates, lutein, and zeaxanthin. And don’t think that white veggies, like mushrooms,
turnips and parsnips, are devoid of these beneficial phytochemicals; they are rich sources of anthoxan-
thins, organosulfur compounds. Carrots, beets, and sweet potatoes are also rich in B vitamins, as are
artichokes, asparagus, okra, broccoli, green peppers, leafy green vegetables, mushrooms, and
cauliflower. Many of these vegetables are also strong sources of vitamins C and K, calcium, chromium,
copper, iron, magnesium, manganese, potassium, sulfur, and zinc.

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by Dr. Sarah Ballantyne, PhD
 Just as it’s important to eat a diversity of colors when choosing plant foods,
it’s also important to switch up the foods you eat within a particular color category.

In fact, it may surprise you to know just how different highly related foods can be when it comes to their
nutritional features. Kale and collard greens are both slightly bitter thick leafy greens from the
cruciferous family of vegetables. They are often prepared in similar ways, and you might see them as
interchangeable in cooking. But while they might substitute nicely for each other in recipes, they
contribute slightly different nutrients to your diet. For example, kale has more vitamin C and K, but
collards contain more vitamins B5 and B9.

When we look at the statistical relationships between vegetable consumption and mortality or disease
risk, it becomes clear that the more vegetables we eat, the more protected we are. For every serving of
vegetables or fruit we consume, we reduce the risk of all-cause mortality (a measurement of overall
health and longevity) by 5%, with the greatest risk reduction seen with 8 servings per day and more.
That means that eating eight servings of a variety of vegetables and fruits per day needs to be seen as a
bare minimum for supporting health. It also means that the more we’re able to increase our vegetable
intake, the more benefits we’ll see reflected in our health.

There’s another reason to pile veggies onto every plate. Whether we analyze hunter-gatherer diets, Blue
Zone diets, or evaluate through the lens of nutritional sciences, we see that our micronutrient needs are
best met when we consume about half of our calories from animal foods (meat, fish and shellfish) and
the other half from plant foods (veggies, fruit, and fresh herbs). But, keep in mind that 50% of dietary
calories coming one type of food isn’t the same as 50% of dietary volume (that is, how much space it
takes up on a dinner plate) coming from that type of food. Meat and other animal foods tend to be much
more energy-dense relative to most plant foods (as an extreme example, 1 cup of beef steak has 338
calories, whereas 1 cup of raw spinach has only 7 calories). That means a meal containing an assort-

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by Dr. Sarah Ballantyne, PhD
 ment of vegetables plus a smaller portion of meat, fish, or
shellfish could easily come out to a 50/50 ratio of calories
from plants to animals—even though it looks like more
two-thirds to three-quarters plant foods to the eye. Hence,
#threequartersveggies.

Vegetables and fruits are also amazing sources of fiber!

Most types of fiber (called fermentable fibers) can be
digested by the bacteria in our intestines (these bacteria
reside mainly in the large intestine, but there are some
in the small intestine, too). In fact, fiber serves two main
functions in the digestive tract: it adds bulk to stool (which
makes it easier to pass), and it feeds the probiotic bacteria
that live there (which benefits us in many ways). When
probiotic bacteria eat fiber, they produce short-chain fatty
acids such as acetic acid, propionic acid, and butyric acid.
These are extremely beneficial energy sources for the body,
including the cells that line the digestive tract, and help to maintain a healthy gut barrier, and immune
cells to improve immune system function. Healthy gut bacteria have many other important beneficial
effects in the body, such as aiding digestion (they release important vitamins and minerals from our
food so we can absorb them) and regulating the immune system.

Fiber has other effects, like regulating peristalsis of the intestines (the rhythmic motion of muscles
around the intestines that pushes food through the digestive tract), stimulating the release of the
suppression of the hunger hormone ghrelin (so we feel more full), and slowing the absorption of
simple sugars into the bloodstream to regulate blood sugar levels and avoid the excess production of
insulin. Fiber also binds to various substances in the digestive tract (like hormones, bile salts, choles-
terol, and toxins) and, depending on the type of fiber, can facilitate either elimination or reabsorption
(for the purpose of recycling, which is an important normal function for many substances like bile
salts and cholesterol), both of which can be extremely beneficial—if not essential—for human health.

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by Dr. Sarah Ballantyne, PhD
 Fiber RDA – Is it Enough?
One of the controversies surrounding fiber is the simple question: how much is enough?
For most of human history, our fiber intake has far exceeded not only the current average intake (about
8 grams per day for Americans), but also the Recommended Daily Allowance (which is 25 grams per day
for women and 30 to 38 grams for men). In fact, it appears the current RDAs are still too low to provide
the full range of benefits that fiber has to offer.

Research has demonstrated, for instance, that eating eight or more servings of vegeta-
bles and fruits daily is the minimum needed to maximize the benefits of these foods.

A variety of studies of hunter-gatherer diets

How Much is a Serving?
show that most hunter-gatherers consume between
40 and 100 grams of fiber per day (with some
populations eating as much as 250 grams per
day!). And that’s typically with only 20 to 35% of
calories coming from plants. The significant
intake of unrefined high-fiber plants, which in
turn provide abundant substrate for the gut
microbiota, is a key feature missing from our
modern menu.

When it comes to fiber, it is exceedingly difficult

to hit the 100-gram mark with the types of veg-
etables and fruits available to most of us. But 40
to 50 grams per day is pretty doable with a little
awareness of which vegetables pack the best fiber
punch (hello roots and tubers!) and a focus on
covering two-thirds to three-quarters of every
plate of food in vegetables.

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by Dr. Sarah Ballantyne, PhD
 HIGH FIBER FRUITS
& VEGETABLES
Fiber per serving (g) Fiber per serving (g)

Apple 11g Cucumber 2.9g

Artichoke hearts 8.4g Green beans 5.6g

Avocado 6.9g Kale 6.7g

Banana 18.3g Kiwi 11.7g

Beets 7.6g Parsnip 14.4g

Blackberries 7.7g
Passion fruit 18.7g
Broccoli 5.3g
Pear 12.2g
Brussels sprouts 7.2g
Plantain 25.5g
Carrots 7.7g
Purple cabbage 5.9g
Cassava 30.4g
Spinach 2.9g
Celery 2.4g
Sweet potato 16.1g
Collards 4.3g
Taro root 21.2g

As you can see, including some starchy veggies and fruit in our diets is a great way to up our fiber
intake compared to only focusing on non-starchy veggies (eating more than 8 servings is also
awesome!). And in fact, provided that your carbohydrates are coming from whole fruits and
vegetables, the 150- to 300-gram range (30 to 60% of a 2,000-calorie diet) is likely adequate from
a fiber consumption standpoint in addition to falling within the balanced macronutrient
range, which will be discussed shortly. Most healthcare providers and scientists would classify
this level as moderate carbohydrate consumption.

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 7 Tips to Eat More Veggies

1. Eat vegetables with every meal. Yes, even breakfast.

2. Gradually increase your serving sizes of vegetables. This
helps your gut microbiota adjust to higher fiber intake,
which makes it easier to digest larger amounts of veggies.
3. Try wilted salads and lightly braised or sautéed greens like
spinach. They are heated for a very short period of time,
but they decrease in volume greatly!
4. Add more vegetables to soups, stews and casseroles.
Canned pumpkin or pureed cauliflower can be used as a
thickener. You can even puree greens to add to a soup to
make them “disappear”.
5. Choose smoothies over vegetable juices. Lettuce and
spinach are mild flavored so you can typically pack several
servings into one smoothie.
6. Raw veggies like celery, carrots and radishes make a great portable snack. Think of
ways you can bring veggies “on the road” with you during the day.
7. Add veggies to dessert! Vegetable smoothies freeze into ice pops very well. Also look
for recipes that use vegetable powders as flour alternatives for baking and treats!

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 Organ Meat is Da Bomb
Compared to muscle meat, organ meat is more densely
packed with just about every nutrient, including heavy
doses of vitamins B1, B2, B6, B9, and the very important
B12. Organ meat is also loaded with minerals like phospho-
rus, iron, copper, magnesium, iodine, calcium, potassium,
sodium, selenium, zinc, and manganese and provides the
important fat-soluble vitamins A, D, E, and K. Organ meat
is known to have some of the highest concentrations of
naturally occurring vitamin D of any food source. Organ
meat also contains high amounts of essential fatty acids,
including arachidonic acid and the omega-3 fats EPA and
DHA.

Liver is one of the most concentrated sources of vitamin A

of any food. In addition to containing dozens of important
vitamins and minerals, it is an outstanding source of vitamin D, vitamin B12 (and other B vitamins), cop-
per, potassium, magnesium, phosphorous, manganese, and iron in the heme form that is readily absorbed
and used by the body. Kidney is particularly high in vitamin B12, selenium, iron, copper, phosphorus, and
zinc. Even though heart is technically a muscle, it also is a superfood. Heart is a concentrated source of
the supernutrient coenzyme Q10 (CoQ10, important for cardiovascular health and also rich in kidney and
liver) and contains an abundance of vitamin A, vitamin B12, folic acid, iron, selenium, phosphorus, and

What About Vitamin A Toxicity?

Vitamin A toxicity is rarely seen in the context of whole foods.
According to the Merck Manual:

“Acute vitamin A toxicity in children may result from taking large doses (>300,000 IU [>
100,000 RAE]), usually accidentally. In adults, acute toxicity has occurred when arctic explor-
ers ingested polar bear or seal livers, which contain several million units of vitamin A.”

“Chronic vitamin A toxicity in older children and adults usually develops after doses of >
100,000 IU (> 30,000 RAE)/day have been taken for months.”

A 4-ounce serving of raw beef liver contains 18,928 IU of vitamin A. Even consuming double
this amount daily is well below the toxicity limits for both acute and chronic vitamin A toxicity.
However, if you’re taking vitamin A in supplement form, it’s worth talking with your healthcare
provider about whether or not to limit organ meat consumption.

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 zinc. It’s the number-one food source of copper. Heart also contains twice as much collagen and elastin
than regular muscle meat (which means that it is rich in the amino acids glycine and proline), which are
essential for connective tissue health, joint health, and digestive health.

If you’re living on a tight budget, organ meat can be an excellent way to incorporate grass-fed meat into
your diet while keeping your spending in check. Even grass-fed organ meat can be significantly cheap-
er than muscle meat. I recommend consuming organ meat at least twice a week, but the more you can
incorporate this nutrient-packed protein, the better!

If you don’t like liver or other organ meats, there are several recipes in this book designed to help you
“hide” the flavor. The spices in these recipes do a nice job of masking the unique taste of these essential
foods. And if organ meat is a complete nonstarter for you, consider adding encapsulate organ meat as a
supplement to your diet.

Studies of modern hunter-gatherers show a great preference for organ meat, which is often given to the
most prized members of the tribe (be it hunters, elders, or sometimes pregnant women).

In some hunter-gatherer cultures, muscle meat is given to the dogs or thrown away and
left for scavengers in times of plenty. And some of the healthiest hunter-gatherer popu-
lations are those that eat predominantly organ meat.
However, when food is scarcer, we see snout-to-tail consumption, meaning that every part of the ani-
mal is consumed and nothing is wasted. This translates to eating a ratio of organ meat to
muscle meat that’s similar to the animal’s own ratio.

How much is that? Approximately 54% of an industrially produced steer and 58% of an industrially
produced hog is considered edible. (The remaining percentage includes parts that are used in other ways
or discarded, such as the hide and bones.) This edible portion includes edible by-products (or offal) and
muscle meat, which is sold as cuts of meat and ground meat or processed into deli meats and sausages.
Typically, offal accounts for approximately 12% of the live weight of cattle and 14% of the live weight of
hogs (when pork rinds [skin] are included as offal and not discarded). Converting this to a ratio, we get:

ºº 24% of the edible portion of a hog is offal

22% of the edible portion of a steer is offal

ºº
How representative are these percentages? Well, pastured pork is leaner, so the percentage of organ
meat to muscle meat will be slightly higher. But even in wild game, such as elk and mule deer, the per-
centage of body weight that is organ meat versus muscle meat is fairly consistent.

The bottom line is the same: about one-fifth to one-quarter of the meat we eat should be offal (that is,
not steak and burgers!). If you eat fish several times a week and meat the rest of the time (and you eat
three meals a day), this translates to about four meals of offal per week.

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 What About Toxins in Liver?
One of the most common misconceptions about liver (and the reason some people are
afraid of eating it) is the belief that this organ acts like a sponge, absorbing and accumulat-
ing toxins as it processes them. In fact, this is part of the rationale behind many “detox di-
ets” that claim to clean out the liver, which is portrayed as getting gunked up with toxins
from unhealthy eating and living.

This couldn’t be further from the truth! In reality, the liver acts more like a self-cleaning
filter than a sponge: it processes and converts toxins into water-soluble products to be
excreted, but it doesn’t serve as a storage space for them. What the liver does store is the
full array of nutrients needed to perform its many functions, including detoxification; for
example, the fat-soluble vitamins A, D, and K; minerals like iron and copper; and vitamin
B12. Liver is a ridiculously nutrient-dense foods (arguably the most nutrient-dense food!)
because it’s a vital, hardworking, multitasking organ! And, it happens to provide you with
the micronutrients that your liver needs to do its job!

What’s more, because the liver has so much enzymatic equipment to break down toxins
(and because of its relatively low fat content, making it less likely to store fat-soluble
chemicals and other contaminants), it may actually be one of the safest organs to eat.

Seafood
Of all the animal products, seafood has one of the most
consistently positive track records in the scientific literature.
For one, fish and shellfish are the richest sources of the long-
chain omega-3 fatty acids DHA and EPA, which block multiple
inflammation pathways in our cells. Deficiencies in these
anti-inflammatory omega-3 fats have been linked to dyslexia,
violence, depression, anxiety, memory problems, Alzheimer’s
disease, weight gain, cancer, cardiovascular disease, stroke,
eczema, allergies, asthma, inflammatory diseases, arthritis,
diabetes, autoimmune diseases, and many others—so it’s easy
to see why getting enough of them is important. In fact,
omega-3s have been confirmed in study after study to reduce
our risk of many chronic diseases and chronic disease risk
factors, such as high triglycerides.

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 Studies evaluating the role of dietary omega-3 fatty acids in human health show that the ratio of
dietary omega-3 to omega-6 fats is far more important than the actual quantities of these fats,
provided that we are eating enough fat to meet our basic needs. An ideal ratio is somewhere between
1:1 and 1:4. However, typical Western diets fall into a range between 1:10 and 1:25! This is largely thanks
to processed vegetable oils, grains, and the higher levels of omega-6 fatty acids that are present in the
meat and dairy from grain-fed animals.

Fish is also high in easily digestible protein, vitamin D, vitamin A, iron, selenium, and
many other essential nutrients that aren’t as abundant in other foods. Wild-caught
saltwater fish have the highest concentrations of vital nutrients, but farmed and
freshwater fish are also excellent sources.
Fresh, frozen, and canned whole fish (such as sardines, tuna, and canned salmon, which are the
cheapest options) are all great choices! Aim for three to five servings of fish per week as a start;
there’s no reason why you can’t enjoy fish daily!

Many people are surprised to learn about the amazing nutritional benefits of shellfish, rivaling the
nutrient-density of liver! Bivalves, including oysters, clams, and mussels, are shellfish with a hinged,
two-part shell. In general, bivalves tend to be rich in vitamin B12, highly digestible complete protein
(as with fish), iron, zinc, copper, calcium, sodium, phosphorus, and selenium, as well as DHA and EPA.
Some, like oysters, are a rich source of vitamin D, and others are off the charts for vitamin B12. (1,648%
of the recommended daily allowance in clams? Yes, please!) But each bivalve has its own unique nu-
tritional profile. Oysters are an amazing source of vitamin D, vitamin B12, copper, zinc, and selenium.
In fact, a mere 100 grams of oysters contains six times the RDA of zinc! Given that anestimated 73%
of us aren’t getting enough zinc and that it plays a fundamental role to play in our health, a serving
of oysters every week goes an incredibly long way toward supporting optimal health. Clams have
particularly high levels of vitamin B12, iron, selenium, and manganese. Scallops are particularly high
in vitamin B12, selenium, zinc, and phosphorus. Mussels are teeming with vitamin B12, selenium, and
manganese (offering over 100% of the RDA for each of them!)

Unless you have an allergy to them, bivalves are an amazing nutrient resource that you should tap into
at least once per week. Aim for at least once serving per week of bivalve shellfish.

Of course, bivalves are not the only shellfish in town! Crab, shrimp, prawns, lobster and crayfish
belong to a different shellfish family, crustaceans. Crustaceans belong to the arthropoda phylum (as
do insects), and feature exoskeletons that moult as they grow, branched limbs, and a larval life stage.
There are about 67,000 different species of crustaceans, mostly aquatic. And while not as impressive
in terms of nutrient content as bivalves, crustaceans still provide substantial amounts of high-quality
protein, omega-3 fats, and important vitamins and minerals.

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 While sea vegetables are rich in essential minerals and vitamins—iodine, calcium, magnesium, iron,
potassium, chromium, selenium, zinc, B vitamins, vitamin C, vitamin E, and vitamin K, to name a few—
the more compelling reason to include them in a nutrient-focused diet at least weekly is the dozens of
additional trace minerals, many of which are depleted in modern soils and therefore insufficient in
vegetables and fruit. If Seaweed Salad isn’t your thing, try replacing salt both for cooking and at the
table with one that includes sea vegetable flakes.

What About Toxins in Fish

and Shellfish?
Fish and shellfish get a bad rap for being full of various toxins, but
most of the time, this is a non-issue.

For the vast majority of fish, mercury is not a concern, because most typically consumed
varieties of ocean fish contain much more selenium than methylmercury. Selenium-bound
methylmercury is not efficiently absorbed by our bodies plus the methylmercury that is
absorbed is already bound to selenium, so it can’t interfere with our selenoenzymes (the
mechanism by which mercury is toxic to our health). In fact, the selenium in seafood
protects us from potential mercury exposure from other sources, too. The only fish that
we need to avoid are those that contain more methylmercury than selenium—a fairly short
list. It includes king mackerel, marlin, pilot whale, shark, tarpin, tilefish, and swordfish,
although some studies show that swordfish is okay.

In general, fish is much lower in dioxins and polychlorinated biphenyls (PCBs) than other
foods (including beef, chicken, pork, dairy products, and vegetables). Depending on the
water it comes from, wild-caught fish is typically lower in dioxins and PCBs than farmed
fish, but even in the case of farmed fish, the health benefits far outweigh the risks,
especially in the context of the importance of DHA and EPA fats for overall health.

Despite fears that our oceans are the most dangerous source of radiation-exposed food
following the Fukushima nuclear plant disaster, marine foods generally deliver much
lower levels of radioactive cesium than terrestrial foods from equally contaminated
environments. In truth, the levels of radiation detected in fish from the Pacific Ocean are
so low that we would need to eat 700,000 pounds of the most radioactive fish in the bunch
just to match the amount of radiation we normally get each year from other sources (about
6.2 millisieverts per year, compared to 100 millisieverts as the lowest yearly dose that’s
been linked to an increased risk of cancer).

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 It’s also a myth that we should limit shellfish consumption over toxin concerns because
they are “bottom-feeders.” Shellfish actually has some of the lowest contaminant rates of
all animal foods!

Bivalves are generally filter-feeders, which means that they use their gills to draw in food
(mostly phytoplankton and microscopic sea creatures) and filter out larger particles. (A
few species are carnivorous and eat larger organisms, but they aren’t the types of bivalves
that humans usually consume—and you’ll probably never find them on a restaurant menu.)
This is much different than sea creatures that act as opportunistic scavengers, consuming
dead animals and large debris, such as wild catfish.

Likewise, because most bivalves are so low on the food chain, they pose a minimal risk in
terms of heavy metal contamination. Large-bodied, long-living sea creatures like sword-
fish and sharks tend to be higher in mercury because they accumulate heavy metals from
their prey. By contrast, bivalves consistently rank as some of the lowest-mercury seafood
available because the particulate matter they consume is nearly free from heavy metals.

As far as toxins go, the main legitimate danger with bivalves is the potential for one of
four types of shellfish poisoning: amnesic, diarrheal, neurotoxic, and paralytic, distin-
guished by the specific toxin that causes the poisoning. When bivalves consume toxin-
producing algae (from harmful algal blooms, or HABs, like red tide), they risk passing on
marine biotoxins to the humans who eat them (namely domoic acid, okadaic acid,
brevetoxins, or saxitoxin). Those toxins can cause a range of respiratory, gastrointestinal,
and neurological symptoms and in some cases can be fatal (although this is rare). Those
toxins aren’t deactivated by heat, so simply cooking shellfish isn’t enough to prevent
poisoning. Shellfish poisoning is really a concern only if you’re planning on harvesting
wild shellfish yourself; you can protect yourself by checking with local authorities as to
the presence of HABs before heading out on your hunt.

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 therapeutic doses of essential vitamins and minerals
exceed the established upper limits.
RDA AI UPPER LIMIT

3,000 IU
Vitamin A 10,000 IU

A Nutrient-Sufficient Diet
2,300 IU

1.2 mg
Vitamin B1 Not established
1.1 mg

1.3 mg
Vitamin B2 Not established
Achieving nutrient-sufficiency is achieved by making these 1.1 mg

16 mg
nutrient-dense powerhouse foods the basis of every meal. This Vitamin B3
14 mg
35 mg

means that every meal would be centered around organ meats, Vitamin B5 5 mg Not established

1.3 mg
shellfish, brightly pigmented fruit, sea vegetables, fatty fish, Vitamin B6
1.3 mg
100 mg

Vitamin B7 30 mcg Not established

cruciferous vegetables, leafy greens, mushrooms, fermented
Vitamin B9 400 mcg 1 g
veggies, fresh herbs, and fibrous roots. Other fruit, vegetables,
Vitamin B12 2.4 mcg Not established

whitefish, grass-fed and pasture-raised meats, and healthy fats 90 mg

Vitamin C 2 g
75 mg
like extra virgin olive oil round out the diet. Eating 8 or more Vitamin D 600 IU 4,000 IU

servings of vegetables per day, seafood most days, and organ Vitamin E 22 IU 1,500 IU

120 mcg
meat 3 to 5 times per week is important for nutrient sufficiency. Vitamin K
90 mcg
Not established

550 mg
Choline 3.5 g

Balanced Macronutrients
425 mg

Calcium 1,000 mg 2.5 g

35 mcg
Chromium Not established
25 mcg
One of the consequences of a nutrients-first approach is that
Copper 900 mcg 10 mg

the distribution of macronutrient intake tends to end up fairly Fluoride

4 mg
10 mg
3 mg
balanced, with roughly a third, give or take, of calories from Iodine 150 mcg 1.1 mg

each of protein, fat and carbohydrate. This is what is referred to 8 mg

Iron 18 mg (18–50 years) 45 mg
as balanced macronutrients¸ meaning that no macronutrient is 8 mg (51+ years)

low or high, i.e., not low-carb, low-fat, high-fat, high-protein, 400 mg (19–30 years)
420 mg (31+ years)
Magnesium Not established
etc. And while the primary nutrient focus of the Autoimmune 310 mg (19–30 years)
320 mg (31+ years)
Protocol is sufficiency of micronutrient and fiber intake, there 2.3 mg
Manganese 11 mg
1.8 mg
are some compelling reasons to avoid the pitfalls of macronu-
Molybdenum 45 mcg 2 mg

trient ratio extremes. Phosphorus 700 mg 4 g

Potassium 4.7 g Not established

Eating too little of any macronutrient can result in malnutri- Selenium 55 mcg 400 mcg

tion. Inadequate fat can decrease our absorption of fat-soluble Zinc

11 mg
40 mg
8 mg

vitamins and deprive us of essential fatty acids. Inadequate

*Only RDAs for adults aged 19 to 50 are shown, except where
protein can reduce lean muscle mass, immune function, bone otherwise noted: are recommendations for adult men and are
recommendations for adult women. See page 425 for RDAs for
mineral density, and cause a host of problems related to babies and children. Visit usda.gov for RDAs for other age groups
as well as recommendations for pregnant and lactating women.
deficiency of essential amino acids. Too few carbohydrates
can mean insufficient fiber and micronutrients abundant invegetables and fruits, including: vitamin C,
B vitamins, vitamin K, potassium, magnesium, chromium, and phytochemicals including polyphenols,
chlorophyll, carotenoids, isothiocyanates, and organosulfur compounds, all of which are important for
disease prevention. The solution? We can balance our macronutrients by eating moderate amounts of
carbohydrate, fat, and protein.

The healthy ratio of calories from fat, carbohydrates and protein can be determined by examining the
overlap between hunter-gatherer macronutrient intakes (adjusted for errors caused by early ethnogra-
phers underestimating plant food intake due to interacting more with male hungers than female

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 gatherers) and the Accepted Macronutrient
Distribution Ranges (AMDR) established by the
Food and Nutrition Board of the Institute of
Medicine (using evidence from interventional
trials with support of epidemiological evidence
that suggest a role in the prevention or
increased risk of chronic diseases, and based
on ensuring sufficient intake of essential
nutrients).

When taken together, you end up with the

following ideal distribution of macronutrient
intake:

~20 to 35% calories from fat

ºº
~20 to 35% calories from protein
ºº
~30 to 60% calories from carbohydrate
ºº
It’s worth emphasizing that these calories
would ideally all come from whole-food
sources and that these ratios do allow for
some wiggle room. For example, people with
one or two copies of the ApoE4 gene may do better with fat intake closer to 15%. Furthermore, studies
that cap healthy fat intake at 35% do not take fat quality into account, so it may be very healthy to have
fat intake upwards of 50% of total calories, provided those fats come from extra virgin olive oil, fish,
and pastured meats. Carbohydrate quality is also important: sugars (even from whole food sources like
fruit) shouldn’t make up more than 25% of total calories (and less than 10% of calories should come from
added sugars, like honey or unrefined cane sugar); and, as already discussed, high fiber intake is a key
aspect of a healthy diet. Additionally, there may be some benefit to some stochasticity in macronutri-
ent intake, highlighting that the occasional day where intake is way off of these ranges is totally okay.
Finally, seasonal variation (typically more protein and fat in the winter, more carbs in the summer) may
also be beneficial. The take-home message: aim for balanced macronutrients; but, if you find that you
feel best outside of these ranges, and provided you aren’t dipping into macronutrient extremes (protein
and fat should not dip below 10% of calories, and carbs should not dip below 20% of calories), go ahead
and listen to your body.

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 What does a balanced-macronutrients
plate look like?

A good rule of thumb for a balanced macronutrient plate:

ºº About 6 to 8 ounces of meat or seafood

ºº ½ to 1 cup of a starchy vegetable like sweet potato
ºº 1 to 2 cups of nonstarchy veggies like broccoli or collards

ºº and ½ cup of fruit for dessert

Go ahead and choose fattier cuts of meat or roast your veggies with a healthy fat, but
don’t go out of your way to add fat to your plate (there’s no need to douse your food
in oil or salad dressing.)

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 Avoid Carb-Phobia
It may surprise you to see recommended carbohydrate intake in the 30% to 60 % of total calories range
when low-carb and ketogenic diets purport to cure just about every possible ill. Between the propagan-
da surrounding low-carb diets and the common pitfall of combining AIP with diets that limit vegetable
consumption (such as keto, GAPS, SCD or the candida diet), some people end up adopting a too-low-carb
version of the AIP, which can hinder healing, cause sleep disturbances, tank metabolism, and generally
have you feeling pretty icky.

When we consume carbohydrates, our blood sugar increases. In response to that rise in blood sugar, the
pancreas releases the hormone insulin, which facilitates the transport of glucose into the cells of the
body and signals to the liver to convert glucose into glycogen for short-term energy storage in liver and
muscle tissues and into triglycerides for long-term energy storage in adipose tissues.

It’s a beautifully efficient system… until things go wrong. Chronically elevated blood sugar levels
stimulate adaptations within cells, rendering them less sensitive to insulin. These adaptations may
include decreasing the number of insulin receptors embedded within cell membranes and suppress-
ing the signaling within cells that occurs after insulin binds to its receptor. This causes the pancreas to
secrete even more insulin to lower the elevated blood glucose levels. This is called insulin resistance or
loss of insulin sensitivity, when more insulin than normal is required to deal with blood glucose. When
normal blood sugar levels can no longer be maintained, you get type 2 diabetes. Insulin resistance is bad.
It increases inflammation and affects metabolism, so it promotes weight gain and increases risk not only
of obesity and diabetes, but also cardiovascular disease, many forms of cancer, asthma, allergies, PCOS,
chronic kidney disease, many autoimmune diseases…. the list goes on.

So, if chronically elevated blood sugar levels makes you insulin resistant leading to health problems,
then the key must be to not eat all those carbs, right? This thinking is what led to the now-debunked
carbohydrate-insulin hypothesis of obesity and a surge in popularity of low-carb diets since the early

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 1990s. The fact is that insulin plays a lot of important roles in human health independent of its role
in energy balance. So, while insulin resistance is clearly damaging, not eating enough carbs to secrete
much insulin can also cause health challenges.

Insulin is a superhormone, with an array of functions in human physiology that far exceed its simplis-
tic characterization as a metabolic hormone. And once we recognize these other roles of insulin, it’s
easy to understand why too little insulin (or hindered insulin signaling as occurs in insulin resistance)
can have negative consequences. Specifically, insulin is important for normal thyroid function, skel-
etal muscle metabolism, bone remineralization, central nervous system health, hormone regulation,
and immune health.

The regularity effects of insulin on the immune system are of particular interest to autoimmune dis-
ease sufferers. The innate immune system is our first line of defense during infection or injury. Various
immune cells (neutrophils, macrophages and natural killer cells) are activated by insulin and rendered
more effective at their jobs. For example, insulin stimulates phagocytosis (the process of engulfing
pathogens) by “eater” cell types. And, insulin enhances the cytotoxicity of cells that destroy virally-in-
fected and cancerous cells. Elevated insulin causes generalized inflammation; however, when insulin
resistance becomes advanced, the activity of these innate immune system cells becomes impaired.

The adaptive immune system recognizes specific pathogens and remembers them, why you only ever
get chicken pox once and why vaccines work. Insulin activates adaptive immune system effector
cells (T cells that drive immune attacks) as well as regulatory cells (T cells that constrain the system),
also rendering these cells more effective. When insulin is high, two subtypes of T cells (Th1 and Th17,
whose overactivity are implicated in allergic, immune and autoimmune conditions) become overactive
while some types of regulatory T cells disappear. Blocking insulin signaling suppresses the activity
and formation of both effector cells and regulatory cells.

Insulin signaling is extremely important for normal immune function. Its specific
effects on immune cells explains why high insulin or insulin resistance is inflammatory,
but also why insulin resistance is associated with allergic, inflammatory and
autoimmune diseases and a reduced ability to fight off infection.

While inflammation is a hallmark of insulin resistance, we also see increased susceptibility to

infection in type 2 diabetes with protracted recovery time. However, the evidence is also mounting
that very low-carbohydrate diets, such as ketogenic diets, have negative effects on our health that are
often analogous to insulin resistance. In diabetes, the body is less sensitive to insulin signaling. During
very low-carb intake, insufficient insulin is secreted for normal signaling. One recent study showed an
increase in C-reactive protein (a blood borne marker of inflammation) during weight loss with a
low-carb, high-fat but not a high-carb diet. Another study in patients with rheumatoid arthritis
showed no benefits to the cytokine IL-6 or T cell numbers and activation with a ketogenic diet. And, in

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 an animal study of malignant glioma, a ketogenic diet increased the numbers and activation of effector
cells (especially Th1) while decreasing the population of regulatory cells. Long-term studies of keto-
genic diets in children and adolescents with epilepsy show a trend towards reduced white blood cells
counts, while also reporting increased susceptibility to serious infection, affecting 10 to 15% of study
participants.

Maintaining insulin sensitivity is essential for health, but avoiding or drastically reducing
carbohydrate intake isn’t necessary. Keeping blood sugar levels within a healthy “happy medium”
range is easy if we limit ourselves to whole-food sources of carbohydrates (like starchy root vege-
tables and whole fruits) and eat them as part of a meal that includes animal protein and nonstarchy
high-fiber veggies (like kale or broccoli). There really isn’t a good argument for limiting vegetable and
fruit intake, including starchy vegetables rich in fermentable substrate that the gut microbiome loves!

For those with insulin resistance or diabetes, measuring carbohydrate portions and keeping track of
post-meal glucose levels is still advisable. It’s important to emphasize though, insulin sensitivity is
also inextricably tied to how much sleep we get, how stressed we are and how active we are. In fact,
studies show that one night of poor sleep causes higher insulin resistance than 6 months of bad diet.
That means that dialing in lifestyle factors is a necessity for restoring and maintaining insulin
sensitivity.

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 Insulin and Thyroid Function
For anyone with autoimmune thyroid disease or subclinical
hypothyroidism (commonly comorbid with autoimmune disease),
eating enough carbs while supporting insulin sensitivity is
doubly important because insulin regulates thyroid hormones.

The thyroid gland produces hormones that control metabolism

as well as influence other essential systems in the human body, such as the cardiovascular
system, the immune system, and calcium homeostasis. Thyroid hormones increase our
basal metabolic rate, control appetite, improve absorption of nutrients from the digestive
tract, and control gut motility. They play an essential role in glucose metabolism and also
stimulate the breakdown of fats.

The prohormone thyroxine (T4) is produced in the thyroid gland and is then converted into
the more active triiodothyronine (T3) by enzymes called deiodinases in multiple areas of
the body. Type 2 deiodinase (D2) is present in the thyroid, central nervous system, pituitary
(making its activity the most important for negative feedback on thyroid-stimulating
hormone, TSH), pineal gland, brown adipose tissue, placenta, skeletal muscle, and heart.
It’s 1000 times more active than other deiodinases, and D2-catalyzed T3 production
increases thyroid hormone signaling (blocking D2 causes localized hypothyroidism in
various tissues). Importantly, its activity is upregulated by insulin and is decreased during
fasting; insulin stimulates the conversion of T4 to T3 via D2 activity.

Insulin resistance, obesity and diabetes are linked with altered thyroid function, but both
hypothyroidism and hyperthyroidism are possible consequences. The prevalence of
thyroid disease, including subclinical hypothyroidism, in patients with obesity or diabetes
is significantly higher than in the general population.

Ketogenic diets decrease thyroid function. In a recent study of pediatric epilepsy patients
following a ketogenic diet for seizure control, participants had an overall decrease in free
T3 and concurrent increase in TSH. A whopping 1 in 6 participants developed hypothyroid-
ism requiring L-thyroxine medication within the first 6 months of the study! And nearly
half of those were within the first month! Of course, weight loss in general can reduce T3,
but this is because T3 tends to be elevated in obesity and weight loss normalizes it. Studies
that have investigated the effect of weight loss via calorie restriction on thyroid function
have not identified an increased risk of hypothyroidism (T3 and TSH remain within normal
lab ranges).

64 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 HEALTHY AIP CARBS
HEALTHY PALEO CARBS
GLYCEMIC INDEX (GI) GLYCEMIC LOAD (GL)
LOW MEDIUM HIGH LOW MEDIUM HIGH

0 20 40 55 70 80 100 0 10 20 30 40 50 60

F RUI TS
When carbohydrates come from whole fruits and vegetables, even
APPLE SERVING SIZE: 120 g (1 medium = 182 g)

Glycemic Index* 36 Glycemic Load 5 Fiber (g) 2.9

and have a low or moderate impact on blood sugar levels. NUTRIENTS: Vitamin C, polyphenols

BANANA SERVING SIZE: 120 g (1 medium = 118 g) GRAPEFRUIT SERVING SIZE: 120 g (1/2 fruit = 123 g)

Glycemic Index* 48 Glycemic Load 11 Fiber (g) 3.1 Glycemic Index* 25 Glycemic Load 3 Fiber (g) 1.9
NUTRIENTS: Vitamins B6 and C, potassium, manganese NUTRIENTS: Vitamin C, carotenoids, betaine

GRAPES SERVING SIZE: 120 g (1 cup = 151 g) KIWI SERVING SIZE: 120 g (1 medium = 76 g)

Glycemic Index* 59 Glycemic Load 11 Fiber (g) 1.1 Glycemic Index* 53 Glycemic Load 6 Fiber (g) 3.6
NUTRIENTS: Vitamins C and K NUTRIENTS: Vitamins C, E, and K, potassium, copper

ORANGE SERVING SIZE: 120 g (1 medium = 130 g) MANGO SERVING SIZE: 120 g (1 cup cubed = 165 g)

Glycemic Index* 45 Glycemic Load 5 Fiber (g) 2.8 Glycemic Index* 51 Glycemic Load 8 Fiber (g) 2.2
NUTRIENTS: Vitamins B9 and C, betaine NUTRIENTS: Vitamins B6 and C

PEACH SERVING SIZE: 120 g (1 medium = 150 g) PEAR SERVING SIZE: 120 g (1 medium = 178 g)

Glycemic Index* 42 Glycemic Load 5 Fiber (g) 1.8 Glycemic Index* 38 Glycemic Load 4 Fiber (g) 3.7
NUTRIENTS: Vitamin C NUTRIENTS: Vitamin C, chromium

PINEAPPLE SERVING SIZE: 120 g (1 cup chunks = 165 g) WATERMELON SERVING SIZE: 120 g (1 cup cubed = 152 g)

Glycemic Index* 59 Glycemic Load 4 Fiber (g) 1.7 Glycemic Index* 72 Glycemic Load 4 Fiber (g) 0.5
NUTRIENTS: Vitamin C, magnesium, bromelain NUTRIENTS: Vitamin C, carotenoids

STARC H Y V EG ETABLE S

ACORN SQUASH**SERVING SIZE: 150 g (1 cup cubed = 205 g) BEET SERVING SIZE: 80 g (1/2cup sliced = 85 g)

Glycemic Index* 75 Glycemic Load 6 Fiber (g) 5.3 Glycemic Index* 64 Glycemic Load 5 Fiber (g) 3.4
NUTRIENTS: Vitamins B1, B3, B5, B6, B9, C, and E, NUTRIENTS: Vitamin B6, manganese, betaine
magnesium, potassium, phosphorous, copper, manganese

BUTTERNUT SQUASH** SERVING SIZE: 150 g (1 cup cubed = 205 g) CARROTS SERVING SIZE: 80 g (1/2cup sliced = 78 g)

Glycemic Index* 72 Glycemic Load 6 Fiber (g) 3.0 Glycemic Index* 39 Glycemic Load 2 Fiber (g) 2.3
NUTRIENTS: Vitamins B1, B3, B6, B9, C, and E, magnesium, NUTRIENTS: Vitamin K, carotenoids
potassium, manganese, carotenoids

CASSAVA, boiled SERVING SIZE: 100 g (1 cup cubed = 206 g) GREEN PLANTAIN**SERVING SIZE: 120 g (1 cup sliced = 154 g)

Glycemic Index* 46 Glycemic Load 12 Fiber (g) 1. 8 Glycemic Index* 40 Glycemic Load 13 Fiber (g) 2.8
NUTRIENTS: Vitamin C, manganese NUTRIENTS: Vitamins B6 and C, magnesium, potassium,
carotenoids

PARSNIP SERVING SIZE: 80 g (1/2cup sliced = 78 g)

SWEET POTATO SERVING SIZE: 150 g (1 cup cubed = 200 g)
Glycemic Index* 52 Glycemic Load 4 Fiber (g) 2.8
Glycemic Index* 61 Glycemic Load 17 Fiber (g) 3.8
NUTRIENTS: Vitamins B9 and C, manganese
NUTRIENTS: Vitamins B6 and C, potassium, manganese,
carotenoids
PUMPKIN SERVING SIZE: 150 g (1 cup cubed = 116g)
TURNIP SERVING SIZE: 150 g (1 cup chopped = 144 g)
Glycemic Index* 75 Glycemic Load 3 Fiber (g) 0.8
Glycemic Index* 62 Glycemic Load 2 Fiber (g) 3.1
NUTRIENTS: Vitamins A, B2, B1, B3, B5, B6, B9, C, and E,
iron, phosphorous, potassium, copper, manganese NUTRIENTS: Vitamin C

TARO SERVING SIZE: 150 g (1 cup sliced = 132 g)

YAM SERVING SIZE: 150 g (1 cup cubed = 136 g)
Glycemic Index* 55 Glycemic Load 4 Fiber (g) 7.7
Glycemic Index* 54 Glycemic Load 20 Fiber (g) 5.8
NUTRIENTS: Vitamins B1, B6, C, and E, magnesium,
phosphorous, potassium, copper, manganese NUTRIENTS: Vitamins B1, B6, and C, potassium, copper,
manganese
RUTABAGA (swede) SERVING SIZE: 150 g (1 cup cubed = 170 g)

Glycemic Index* 72 Glycemic Load 7 Fiber (g) 2. 7

NUTRIENTS: Vitamin C, magnesium, phosphorous,
potassium, manganese

* Glucose = 100 ** Plantains and winter squash are technically fruits, but they cook like vegetables, which is why they are grouped with other veggies in this table.

65 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 The AIP Food Groups
The first criterion for choosing foods is nutritional merit. Eating a wide variety of foods from all of
these food groups, as well as other vegetables and fruit, is the best strategy to make sure that your
diet is micronutrient sufficient.

O R GA N M EA TS

Complete protein Creatine Vitamin B2

ºº ºº ºº
Healthy fats DHA and EPA (when Vitamin B3
ºº ºº grass-fed) ºº
Alanine Vitamin B5
ºº Glycine ºº
ºº
Arginine
ºº ºº
Vitamin B7
Iron
ºº
Biotin
ºº ºº
Vitamin B9
Molybdenum
ºº
Calcium
ºº ºº
Vitamin B12
Phosphorus
ºº
Chlorine
ºº ºº
Vitamin C
Proline
ºº
Choline
ºº ºº
Vitamin D
Selenium
ºº
Chromium
ºº ºº
Vitamin E
Sulfur
CLA (when
ºº grass-fed) ºº ºº
Vitamin K
Ubiquinol
ºº ºº
Zinc
Cobalt Vitamin A
ºº ºº
Copper Vitamin B1
ºº ºº

M EA T A N D P O U LT R Y

Complete protein Glycine Vitamin B2

ºº ºº ºº
Healthy fats Iron Vitamin B3
ºº ºº ºº
Alanine Phosphorous Vitamin B5
ºº ºº ºº
Arginine Proline Vitamin B6
ºº ºº ºº
CLA (when Selenium Vitamin B12
ºº grass-fed) ºº ºº
Sulfur Zinc
Creatine ºº ºº
ºº ºº
Ubiquinol
DHA and EPA
ºº (when grass-fed) ºº
Vitamin B1

66 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 FI S H
Complete protein Iron Vitamin B1
ºº Healthy fats ºº Magnesium ºº Vitamin B2
ºº Alanine ºº Manganese ºº Vitamin B3
ºº Arginine ºº Phosphorus ºº Vitamin B5
ºº Calcium ºº Potassium ºº Vitamin B6
ºº Choline ºº Proline ºº Vitamin B9
ºº Creatine ºº Selenium ºº Vitamin B12
ºº DHA & EPA ºº Sulfur ºº Vitamin D
ºº Glycine ºº Ubiquinol ºº Vitamin E
ºº Iodine ºº Vitamin A ºº Zinc
ºº ºº ºº

S H E L L FI S H

Complete protein Glycine Vitamin A

ºº Healthy fats ºº Iodine ºº Vitamin B1
ºº Alanine ºº Iron ºº Vitamin B2
ºº Arginine ºº Magnesium ºº Vitamin B3
ºº Calcium ºº Manganese ºº Vitamin B6
ºº Choline ºº Phosphorus ºº Vitamin B9
ºº Cobalt ºº Potassium ºº Vitamin B12
ºº Copper ºº Proline ºº Vitamin C
ºº Chromium ºº Selenium ºº Vitamin D
ºº Creatine ºº Sulfur ºº Zinc
ºº DHA & EPA ºº Ubiquinol ºº Trace minerals
ºº ºº ºº

S EA V E G E TA B L E S

Fiber (more soluble) Iron Vitamin B3

ºº Calcium ºº Iodine ºº Vitamin B5
ºº Carotenoids ºº Magnesium ºº Vitamin B9
ºº Chlorine ºº Manganese ºº Vitamin C
ºº Copper ºº Phosphorus ºº Vitamin E
ºº DHA and EPA ºº Vitamin B1 ºº Vitamin K
ºº Glycine ºº Vitamin B2 ºº Trace minerals
ºº ºº ºº

67 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 L EA F Y G R E E N S

Fiber Flavonoids Vitamin B2

ºº (more insoluble) ºº ºº
Iron Vitamin B3
Boron ºº ºº
ºº ºº
Magnesium
ºº
Vitamin B6
Calcium
ºº ºº
Manganese
ºº
Vitamin B9
Carotenoids
ºº Molybdenum
ºº Plant sterols ºº
Vitamin C
Chlorine
ºº ºº & stanols Vitamin E
ºº Vitamin K
Choline
ºº Potassium ºº
ºº
Chromium
ºº Polyphenols
ºº
Copper
ºº

C R U C I FE R O U S V E G E TA B L E S

Fiber Glycine Proline

ºº (more insoluble) ºº ºº
Isothiocynates Silicon
Boron ºº ºº
ºº ºº
Magnesium
ºº
Sulfur
Calcium
ºº ºº
Manganese
ºº
Ubiquinol
Carotenoids
ºº Molybdenum
ºº Plant sterols ºº
Vitamin B6
Choline
ºº ºº & stanols ºº
Vitamin B9
Chromium
ºº Polyphenols ºº
Vitamin C

ºº
Dithiolethiones
ºº Potassium ºº
Vitamin K

ºº
Flavonoids
ºº
R O OT V E G E TA B L E S A N D WI N T E R S Q UA S H

Fiber (more soluble) Glycine Vitamin B1

ºº ºº ºº
Slow-burning Magnesium Vitamin B2
ºº starchy ºº ºº
Manganese Vitamin B3
carbohydrates ºº ºº
Phosphorous Vitamin B5

ºº
Biotin ºº ºº
Plant sterols Vitamin B6

ºº
Calcium ºº & stanols ºº
Vitamin B9

ºº
Carotenoids
Polyphenols
ºº
Copper ºº ºº
Vitamin C

ºº Potassium
Flavonoids ºº ºº
Vitamin K

ºº

68 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MUSHROOMS

Fiber Plant sterols & Vitamin B3

ºº (more insoluble) ºº stanols ºº
Vitamin B5
Chromium Potassium ºº
ºº ºº ºº
Vitamin B6
Copper Selenium
ºº ºº ºº
Vitamin C
Phosphorous Vitamin B1
ºº ºº ºº
Vitamin D
Vitamin B2
ºº
BERRIES

Fiber (more soluble) Plant sterols and Vitamin B9

ºº ºº stanols ºº
Copper Vitamin C
ºº Polyphenols
ºº
ºº
Flavonoids
ºº ºº
Vitamin E
Potassium
ºº
Iron
ºº ºº
Vitamin K
Vitamin B3
ºº
Magnesium
ºº ºº
Zinc
Vitamin B6
ºº
Manganese
ºº
CITRUS FRUIT

Fiber (about equal Plant sterols Vitamin B5

ºº proportions of ºº & stanols ºº
Vitamin B6
soluble & insoluble)
Polyphenols ºº
Calcium ºº ºº
Vitamin B9

ºº ºº
Potassium
Vitamin C

ºº
Carotenoids
Vitamin B1 ºº
Flavonoids ºº
ºº
O L I V E S A N D OT H E R H I G H - FA T F R U I TS

Fiber (more Magnesium Vitamin B5

ºº insoluble) ºº ºº
Manganese Vitamin B6
Healthy fats
ºº ºº
ºº ºº
MUFA
ºº
Vitamin B9
Boron
ºº ºº
Phosphorous
ºº
Vitamin C
Chlorine
ºº ºº
Potassium
ºº
Vitamin E
Choline
ºº ºº
Vitamin B1
ºº
Vitamin K
Copper
ºº ºº
Vitamin B2
ºº
Zinc
Iron
ºº ºº
Vitamin B3

69 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 O N I O N S , GA R L I C , A N D O T H E R A L L I U M S

Fiber Manganese Sulfur

ºº (more soluble) ºº ºº
Phosphorus Vitamin B1
Choline ºº ºº
ºº Plant sterols and
ºº stanols ºº
Vitamin B6
Diallyl sulfide
ºº ºº
Vitamin B9
Flavonoids Potassium
ºº ºº ºº
Vitamin C

70 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 NUTRIENT SUPERSTARS
FOR IMMUNE HEALTH
While every nutrient plays a role in the immune system, a few stand out as being especially important.
It’s particularly vital to get enough of these immune system superheroes in your diet!

Vitamin A
Vitamin A is a fundamental nutrient, involved in many, many diverse functions in the human body, from
bone health to ocular health to immune health. Vitamin A levels have a profound effect on different T
cell subpopulations, cytokines, and production of various antibody subclasses. Most importantly, vitamin
A (in the form of retinoic acid) supports regulatory T cell formation (by stimulating the differentiation of
CD4+ T cells into regulatory T cells in the thymus).

A B U N D A N T I N:
Fish
ºº Liver
ºº Shellfish
ºº
Vitamin B6
Vitamin B6 is critical for the methylation cycle (defects in methylation increase risk of autoimmune
disease). Vitamin B6 is converted into the coenzyme form pyridoxal 5’-phosphate (PLP), which is used
in the metabolism of amino acids and lipids and is required for gluconeogenesis (the creation of glucose
from amino acids or fatty acids). PLP is also involved in the synthesis of neurotransmitters and
hemoglobin.

A B U N D A N T I N:
Leafy greens
ºº Root vegetables
ºº Red meat
ºº

71 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Vitamin B9
Vitamin B9 (folate) is critical for the methylation cycle (defects in methylation increase risk of autoim-
mune disease. Vitamin B9 is converted into the coenzyme tetrahydrofolate (THF), which is involved in
the metabolism of nucleic acids and amino acids. THF is also necessary for normal cell division and for
the production of red blood cells.

A B U N D A N T I N:
Avocados
ºº
Beets
ºº
Green vegetables
ºº
Vitamin B12
Vitamin B12 is critical for the methylation cycle (defects in methylation increase risk of autoimmune
disease. It is also is essential for the metabolism of carbohydrates, proteins, and lipids in every cell of
the body. It is particularly important for DNA synthesis and regulation, fatty acid synthesis, and energy
production, and plays a key role in the production of blood cells, nerve sheaths, and proteins.

A B U N D A N T I N:
Fish
ºº
Shellfish
ºº
Red meat
ºº
Vitamin C
Vitamin C is an extremely important antioxidant. Adequate levels are essential for preventing gastritis
(whether the cause is autoimmune, chemical, or infectious) and are helpful in controlling persistent in-
fections like H. pylori. Its antioxidant properties seem to be important in controlling the damage caused
by the oxidants produced by inflammatory cells.

A B U N D A N T I N:
Berries
ºº
Citrus fruits
ºº
Dark leafy greens
ºº

72 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Vitamin D
Vitamin D is also crucial for regulating several key components of the immune system, including for-
mation of important antioxidants and controlling subpopulations of T cells. Most important, regulatory
T cell function is dependent on vitamin D (meaning that regulatory T cells can’t perform their duties
without vitamin D). In addition, vitamin D decreases Th1 cells and is known to help balance Th1 and Th2
cell populations. Vitamin D also modulates activity of macrophages, dendritic cells, and both T cells and
B cells.

A B U N D A N T I N:
Fish
ºº
Liver
ºº
Mushrooms
ºº
Vitamin E
Vitamin E’s main role in the immune system appears to be its antioxidant activity, but it has also been
shown to promote maturation of T cells in the thymus. Perhaps most important in the context of
autoimmune disease, vitamin E appears to influence positive selection in the thymus gland, meaning
that vitamin E deficiencies have profound effects on both the relative numbers of the different types of
T cells and on their ability to perform their respective functions.

A B U N D A N T I N:
Avocados
ºº
Leafy greens
ºº
Fish
ºº
Vitamin K2
Vitamin K2 has antioxidant and anti-inflammatory properties. Increased dietary intake of vitamin K2
reduces the risk of coronary heart disease, aortic atherosclerosis, and even all-cause mortality. In a
study of multiple sclerosis in animals, supplementation with vitamin K2 improved symptoms,
inflammation, and immune function.

A B U N D A N T I N:
Fermented vegetables
ºº
Fish
ºº
Liver
ºº

73 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Copper
Copper is necessary for the production of RNA, phospholipids and adenosine triphosphate (ATP, the basic
energy molecule of all cells) and for protein metabolism. Copper is required by the immune system to
support the production of some cytokines by T cells and regulate T cell proliferation (cell division), and
dietary copper is important in resistance to infection.

A B U N D A N T I N:
Mushrooms
ºº
Organ meat
ºº
Shellfish
ºº

Iodine
Iodine is important for the development and proper function of the thyroid and is an essential compo-
nent of thyroid hormones, which themselves regulate immune function. Immune cells that phagocytose
(eating of pathogens) produce various iodoproteins (proteins containing iodine), including T4 thyroid pro-
hormone.

A B U N D A N T I N:
Fish
ºº
Shellfish
ºº
Sea vegetables
ºº

Iron
Iron is a critical component of hemoglobin, the protein in red blood cells responsible for carrying oxygen
from the lungs to every other cell in the body. Specifically, iron is part of a molecule called heme: four
heme molecules are part of a hemoglobin protein, and it is the iron itself that binds to oxygen. Hemoglo-
bin is not the only protein in the body that contains heme. Heme is also a critical component of a family
of proteins (cytochrome p450) involved in protection from oxidative damage and detoxification.

A B U N D A N T I N:
Dark leafy greens
ºº
Liver
ºº
Red meat
ºº

74 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Magnesium
More than three hundred different enzymes in your cells need magnesium to work, including every
enzyme that uses or synthesizes ATP and including enzymes that synthesize DNA and RNA. Magnesium
is also a cofactor in methylation and is necessary for detoxification functions.

Importantly, magnesium depletion has been shown to have a profound impact on the thymus gland and
higher levels of dietary magnesium have also been correlated with decreased systemic inflammation.

A B U N D A N T I N:
Avocados
ºº
Green vegetables
ºº
Fish
ºº
Selenium
Selenium deficiency increases risk of viral infections, it appears to be essential for T cell function (this
has been best studied in the context of HIV infection) and activation of neutrophils and natural killer
cells, and it protects against several inflammatory cytokines and modulates the production of several
key inflammation-signaling molecules. Selenium helps protect against the toxic effects from arsenic,
cadmium, and mercury. Selenium is also a component of one of the body’s most important antioxidant
enzyme, glutathione peroxidase.

A B U N D A N T I N:
Fish
ºº
Poultry
ºº
Red meat
ºº
Zinc
Zinc is the second most abundant metal in the body, after iron, and is necessary for the activity of ap-
proximately three hundred different enzymes. It is required for a healthy immune system, including
through control of T cell development and activation. It has also been shown to reduce cytokine produc-
tion by Th1 and Th17 cells (overactivation of these cells in common in autoimmune disease). Zinc defi-
ciency is arguably the most common micronutrient deficiency in autoimmune disease.

A B U N D A N T I N:
Oysters
ºº
Red meat
ºº
Poultry
ºº

75 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 DHA and EPA
When incorporated into the cell membrane, DHA and EPA affect its properties such as fluidity, flexibili-
ty, permeability, and alter the activity of enzymes that are embedded in the membrane. These effects are
beneficial to the health and function of the cell. For example, having a more flexible and fluid membrane
for a phagocytic cell (an “eater” cell like a macrophage, dendritic cell, or a neutrophil) means that it is
efficient at doing its job of “eating up” pathogens. EPA and DHA are also metabolized to produce prosta-
glandins, thromboxanes, and leukotrienes, important intra- and intercellular signaling molecules. The
prostaglandins, thromboxanes, and leukotrienes formed from EPA and DHA are either anti-inflammato-
ry (and anti-thrombotic) or much less inflammatory (and thrombotic) than those formed by arachidonic
acid (AA, an omega-6 fatty acid).

A B U N D A N T I N:
Fish
ºº Shellfish
ºº Sea vegetables
ºº
Glycine
Glycine regulates both the innate and adaptive immune systems. It inhibits activation of several immune
cells, including macrophages, neutrophils, T cells and monocytes, meaning that without adequate gly-
cine, the immune system is more easily activated. Animal experiments have shown dietary glycine to be
protective in various models of inflammation.

A B U N D A N T I N:
Bone broth
ºº Fish
ºº Red meat
ºº
Glutamine
Glutamine is essential for gut barrier health and microbiome diversity, but it’s also used by immune cells
as a fuel source and supports normal lymphocyte proliferation (cell division) and production of cyto-
kines by both lymphocytes and macrophages. Glutamine demonstrates anti-inflammatory properties
and supplementing with glutamine has been shown to be beneficial in critical care medicine, to modulate
the immune response during Systemic Inflammatory Response Syndrome (SIRS) and sepsis.

A B U N D A N T I N:
Fish
ºº Poultry
ºº Red meat
ºº

76 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Insoluble fiber
Insoluble fiber and soluble fiber support immune health by improving the composition of the gut mi-
crobiome. While high fiber diets are known to reduce inflammation, the effect is stronger for insoluble
fiber than for soluble. Insoluble fiber further improves insulin sensitivity (which is linked to immune
function), supports reabsorption of bile acids, aids detoxification, and is essential for regulating hunger
hormones, especially ghrelin, which is itself an immune modulator.

A B U N D A N T I N:
Celery
ºº
Cruciferous vegetables
ºº
Leafy greens
ºº

Soluble fiber
Soluble fiber supports immune health by improving the composition of the gut microbiome, in particular
by supporting the growth of key probiotic bacteria from the Lactobacillus and Bifidobacterium genera.
Soluble fiber also provides fermentable substrate for the production of short-chain fatty acids by gut
bacteria, linked to diverse health benefits including immune function.

A B U N D A N T I N:
Root vegetable
ºº
Fruit
ºº
Mushrooms
ºº
Plant phytochemicals
There’s over 5000 identified phytochemicals and science has only scratched the surface of how they can
improve our health. Certain phytochemicals have the ability to slow the growth of cancer cells, help
regulate hormones, prevent DNA damage, protect against oxidative stress, reduce inflammation, and
induce apoptosis (death) in damaged cells (like a spring cleanup)—just to name a few of their beneficial
activities. Their antioxidant activity is beneficial for immune function.

A B U N D A N T I N:
Berries
ºº
Cruciferous vegetables
ºº
Leafy greens
ºº

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by Dr. Sarah Ballantyne, PhD
 TOP FOOD SOURCES OF
ESSENTIAL NUTRIENTS
ESSENTIAL AND IMPORTANT
(AND WHERE NUTRIENTS
TO GET THEM)
(AND WHERE TO GET THEM)

VITAMIN A VITAMIN C IRON

Abundant in: Fish Liver Shellfish Abundant in: Berries Citrus Dark leafy Abundant in: Dark leafy Liver Red meat
fruits greens greens

VITAMIN B1 VITAMIN D MAGNESIUM

Abundant in: Nuts & Pork Asparagus Abundant in: Fish Liver Mushrooms Abundant in: Avocados Green Fish
seeds vegetables

VITAMIN B2 VITAMIN E PHOSPHORUS

Abundant in: Organ Red Nuts & Abundant in: Avocados Leafy Fish Abundant in: Seafood Nuts & Red meat
meat meat seeds greens seeds

VITAMIN B3 VITAMIN K1 POTASSIUM

Abundant in: Organ Poultry Seafood Abundant in: Dark leafy Cruciferous Asparagus Abundant in: Leafy Root Bananas
meat greens vegetables greens vegetables

VITAMIN B5 VITAMIN K2 SELENIUM

Abundant in: Mushrooms Liver Egg yolks Abundant in: Fermented Nuts & Liver Abundant in: Fish Poultry Red meat
vegetables seeds

VITAMIN B6 CALCIUM ZINC

Abundant in: Leafy Root Red meat Abundant in: Leafy greens Nuts & seeds Fish* Abundant in: Oysters Red meat Poultry
greens vegetables *(especially canned fish with the bones)

VITAMIN B7 CHLORIDE TRACE MINERALS

Vegetables
grown in
Abundant in: Egg yolks Organ Fatty fish Abundant in: Seaweed Celery Leafy Abundant in: Unrefined Sea quality
meat greens sea salt vegetables organic soil

VITAMIN B9 CHROMIUM DHA AND EPA

Abundant in: Avocados Beets Green Abundant in: Shellfish Nuts (especially Pears Abundant in: Fish Liver Sea
vegetables Brazil nuts) vegetables

VITAMIN B12 COPPER MONOUNSATURATED

FATS
Abundant in: Fish Shellfish Red meat Abundant in: Mushrooms Organ meats Shellfish Abundant in: Olives & Avocados & Macadamia
olive oil avocado oil nuts

CHOLINE IODINE ALANINE

Abundant in: Egg yolks Organ Grass-fed Abundant in: Fish Shellfish Sea Abundant in: Seafood Red meat Poultry
meat dairy vegetables

ARGININE METHIONINE CoQ10

Abundant in: Red meat Seafood Nuts & Abundant in: Fish Red meat Poultry Abundant in: Fatty fish Heart Red meat
seeds

ASPARAGINE PHENYLALANINE L-CARNITINE

Abundant in: Red meat Poultry Nuts & Abundant in: Red meat Poultry Seafood Abundant in: Rad Meat Fish Poultry
seeds

ASPARTIC ACID PROLINE LYCOPENE

Abundant in: Shellfish Wild game Avocados Abundant in: Red meat Poultry Seafood Abundant in: Tomatoes Red & orange fruits
& vegetables

CYSTEINE SERINE POLYPHENOLS

78 THE AUTOIMMUNE
Abundant in: Red meat PROTOCOL
Poultry Eggs Abundant in: Red meat Poultry Seafood Abundant in: Herbs Berries Dark

by Dr. Sarah Ballantyne, PhD chocolate

GLUTAMINE THREONINE QUERCETIN

 Abundant in: Red meat Poultry Nuts & Abundant in: Red meat Poultry Seafood Abundant in: Rad Meat Fish Poultry
seeds

ASPARTIC ACID PROLINE LYCOPENE

Abundant in: Shellfish Wild game Avocados Abundant in: Red meat Poultry Seafood Abundant in: Tomatoes Red & orange fruits
& vegetables

CYSTEINE SERINE POLYPHENOLS

Abundant in: Red meat Poultry Eggs Abundant in: Red meat Poultry Seafood Abundant in: Herbs Berries Dark
chocolate

GLUTAMINE THREONINE QUERCETIN

Abundant in: Fish Red meat Poultry Abundant in: Dairy Fish Red meat Abundant in: Apples Berries Cruciferous
products vegetables

GLUTAMIC ACID TRYPTOPHAN RESVERATROL

Abundant in: Seafood Red meat Poultry Abundant in: Eggs Seafood Poultry Abundant in: Grapes & Berries Dark
red wine chocolate

GLYCINE TYROSINE TAURINE

Abundant in: Bone broth Seafood Red meat Abundant in: Poultry Fish Nuts & Abundant in: Seafood Dairy Eggs
seeds products

HISTIDINE VALINE PLANT PHYTOCHEMICALS

Abundant in: Red meat & Fish Dairy Abundant in: Dairy Nuts & Seafood Abundant in: Cruciferous Leafy
poultry products products seeds Berries vegetables greens

ISOLEUCINE CARNOSINE INSOLUBLE FIBER

Abundant in: Seaweed Poultry Fish Abundant in: Red meat Fish Poultry Abundant in: Celery Cruciferous Leafy
vegetables greens

LEUCINE CREATINE SOLUBLE FIBER

Abundant in: Fish Red meat Nuts & Abundant in: Red meat Poultry Seafood Abundant in: Root Apples Dried beans
seeds vegetables & lentils

LYSINE

Abundant in: Red meat Poultry Fish

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by Dr. Sarah Ballantyne, PhD
 GUT HEALTH QUICK-START
GUT HEALTH QUICK-START GUIDE
REMOVE THE BIGGEST OFFENDERS: EAT MORE:

Grains Gluten Legumes Nightshades NSAIDs Seafood Starchy roots Leafy Cruciferous Fermented
and tubers greens veggies foods

ANTIBIOTICS also Aim for a 1:1 to 1:4 ratio

cause damage to of omega-3 to omega-6
gut bacteria, so polyunsaturated fats.
Alcohol Sugar Excess they should be used Organ meat Bone broth Avoid consuming more than 40
substitutes sugar only when truly to 50 percent of calories from fat,
necessary, and not and limit saturated fat intake to
for the treatment of 10 to 15 percent of calories.
viral infections. For
more information on
MEAL HYGIENE:
antibiotic use
Processed Emulsifiers High Try drinking a mildly acidic
and fast and saturated fat beverage with meals, like
foods thickeners lemon juice in mineral water. Drink plenty
of water
Avoid drinking too much throughout
with meals (but drink the day.
more between meals).
NOTES ON FIBER AND FERMENTED FOODS:

Aim for at least eight servings of vegetables

per day.

Choose some type of fermented food daily;

mix it up! Chew food
thoroughly.
Ramp up your vegetable consumption slowly,
adding half a serving of vegetables every few Don’t eat Take your time eating;
days until you reach eight servings. when stressed don’t rush to finish your
or distressed. food or eat on the run.
Ramp up your fermented food consumption
slowly, starting with as little as half a Eat two or three distinct meals per day.

teaspoon of fermented food and adding an Each meal should include a protein and two to

additional teaspoon every few days until you four servings of a few different vegetables.

reach a full serving. Avoid grazing Don’t get up and rush

and minimize around immediately
Opt for smoothies, puréed soups, and well-
snacking. after a meal.
cooked veggies if high vegetable consumption
causes gastrointestinal symptoms or poor Avoid eating immediately
stool quality. before or after strenuous
exercise.
Choose more starchy tubers if you’re
experiencing loose stools.

Eat more leafy greens and make sure you’re

well hydrated if your stools are too firm.

LIFESTYLE:
Get plenty Reduce/manage Assume a squatting position If necessary and
of sleep stress when using the toilet (a special not contraindicated,
footstool can help with this) Betaine support digestion
HCl
to align your lower intestines with supplements
properly for efficient defecation
and to minimize strain.

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 GUT HEALTH SUPERFOODS
What makes a food a gut health superfood? Any food that increases microbial diversity of the gut microbi-
ome and supports the growth of key probiotic strains (like Lactobacillus and Bifidobacterium) is definitely
a winner! Additionally, foods rich in nutrients known to improve gut barrier health are beneficial not just
for the gut, but also for immune regulation and whole-body health.

VEGETABLES & FRUIT are rich in diverse types of fiber (which feeds diverse strains of
bacteria because different bacteria have different substrate, i.e., food, preferences) and poly-
phenols (which also support microbial diversity and increase growth of key probiotic strains).
When fruit and vegetable fiber is fermented by our gut bacteria, it produces
short-chain fatty acids (acetate, butyrate and propionate), which are extremely beneficial
energy sources for gut barrier and immune cells.

ROOTS & TUBERS like sweet potatoes and cassava contain fiber types that increase butyr-
ate production. Among its many benefits for our health, butyrate enhances gut barrier integri-
ty and helps combat leaky gut. Butyrate works by upregulating AMP-activated protein kinase
(AMPK) activity, which in turn accelerates the assembly of tight junctions (the complex struc-
tures that help glue gut barrier cells together).

CRUCIFEROUS VEGGIES improve gut microbiome composition even when the intake of
fruits and vegetables is held constant, indicating that cruciferous veggies are
beneficial above and beyond other veggies, likely attributable to their glucosinolate content.
Crucifers contain indole, which helps fight leaky gut by reducing the production of proin-
flammatory cytokines and by increasing the expression of genes that help produce mucin and
strengthen the mucosal barrier. Studies show that indole improves epithelial barrier integrity.

ALLIUMS are rich in inulin fiber, a highly fermentable fiber type that feeds key probiotic
strains as well as a type of flavonoid polyphenol called quercetin, which not only promotes
microbiome composition associated with leanness, but also can cause structural modifications
of the tight junction complexes that leads to a more robust gut barrier.

MUSHROOMS are neither a plant nor an animal; they’re a fungus! As such, they contain
types fiber that are completely unique in our food supply, which explains why mushrooms are
so uniquely beneficial for improving the healthy and diversity of the gut microbiome. Some
compounds in mushrooms are also able to directly modulate the immune system and direct-
ly improve gut barrier health. Mushroom supplementation has even been shown (in mice, at
least) to reverse gut dysbiosis!

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 LEAF Y GREENS contain unique fermentable sugars called sugar sulfoquinovoses, which pref-
erentially feed probiotic strains of bacteria (such as the good kind of E. coli) thereby limiting the
ability of bad bacteria to colonize the gut

ROSACEAE, OR APPLE FAMILY, (includes apples, pears, quince) are rich in polyphenols
and pectin fiber, synergistically increasing production of short-chain fatty acids, and supporting
growth of key probiotic strains (including Bifidobacterium, Lactobacillus, and Faecalibacterium
prausnitzii) while reversing gut dysbiosis (at least in rats).

BERRIES contain bioactive compounds that selectively inhibit pathogenic bacteria, especially
Staphylococcus, but also Salmonella and Listeria. Blueberries, in particular, enhance the growth
of key probiotic strains while also while reducing the transport of endotoxin (an extremely in-
flammatory bacterial protein) across the gut barrier and into the body.

CITRUS Pectin (from lemon) stimulates butyrate-producing bacteria (Ruminococcaceae and

Succinivibrionaceae) and enhances levels of acetic acid and butyrate. Orange pulp and peel
suppress the growth of Escherichia coli O157:H7 and Salmonella Typhimurium Juice from two
orange varieties (cara cara and Bahia) increased abundance of Mogibacteriaceae, Tissierellaceae,
Veillonellaceae, Odoribacteraceae, and Ruminococcaceae.

EXTRA VIRGIN OLIVE OIL increases gut microbial diversity, supports a microbiome pro-
file associated with leanness and a healthy metabolism, and increases growth of key probiotic
strains. This is attributable both to the oleic acid content of olive oil and to the high polyphenol
content.

HONEY contains compounds that act as a selective prebiotic for lactic acid bacteria belonging
to Lactobacillus and Bifidobacterium, while also inhibiting the growth of undesirable micro-
organisms that can act as pathogens. Other bee products--propolis and royal jelly--also support
key probiotic strains of bacteria while inhibit growth of pathogens and bee propolis has also
been shown to increase gut microbial diversity.

GREEN & BL ACK TEA polyphenols (including epicatechin, catechin, 3-O-methyl gallic
acid, gallic acid, and caffeic acid) and their metabolites have been shown to selectively repress
the growth of certain undesirable gut microbes (like Clostridium difficile) while increasing the
growth of probiotic strains like Bifidobacterium species and Lactobacillus species, and increases
production of short-chain fatty acids.

CRICKETS AND OTHER INSECTS contain a unique fiber type in their mineral-rich
exoskeletons. Studies show that consumption this type of fiber (chitin) protects the gut barrier,
promotes the growth of beneficial microbes (including Bifidobacterium, Lactobacillus, Akker-
mansia, and Bacteroides) while also decreasing the abundance of microbes linked with inflam-
mation. Studies of cricket protein supplementation show similar benefits (hello 5.7-fold increase
in Bifidobacterium animalis abundance!) as well as lower levels of inflammation.

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 BONE BROTH is rich in several amino acids important for gut barrier function: glycine (which
is also an important anti-inflammatory amino acid), glutamine and arginine. In fact, glutamine
deficiency itself can cause increased intestinal permeability.

FISH is rich in vitamin A and vitamin D which are both essential for gut barrier health but also
improve gut microbiome composition. Fish is our best dietary source of omega-3 fats, which in-
crease gut microbial diversity and can even reverse gut dysbiosis. In addition, the protein in fish
is uniquely beneficial for the gut microbiome, above and beyond any other type of protein.

SHELLFISH offers many of the same gut barrier health benefits as fish, with the addition
of being rich in zinc (especially oysters!) In addition to its essential role in immune health, zinc
affects the composition of the gut microbiome (zinc deficiency causes loss of microbial diversi-
ty) and the integrity of the gut barrier (zinc deficiency causes increased intestinal permeability).
Zinc has a targeted effect on tight junction proteins and helps regulate their permeability, and
can also offset the effects of agents that impair barrier integrity (such as proinflammatory cyto-
kines).

FERMENTED FOODS help to inoculate the gut with new strains of probiotic
organisms. Wild ferments are best: a wild-fermented sauerkraut can contain upwards of 686
(!) different strains of beneficial bacteria and yeast! You’ll get exposed to different strains with
every new batch of a wild-fermented vegetable. Plus, kombucha and water kefir have their own
signature probiotic strains, including beneficial yeast (Saccharomyces boulardi can inhibit the
growth of candida), so the more variety in fermented foods, the better!

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 What Do I Eat on the AIP?
Some foods are obvious wins for a health-promoting diet because they have tons of beneficial constit-
uents and very few or no constituents that undermine health—good examples of these superfoods are
organ meats, seafood, and most vegetables. Other foods are obvious fails because they have a relative
lack of health-promoting constituents and are rife with problematic compounds—good examples are
gluten-containing grains, peanuts, and most soy products. But many foods fall into the amorphous world
of gray in between these two extremes. Tomatoes, for example, have some exciting nutrients, but they
also contain several compounds that are so effective at stimulating the immune system that they have
been investigated for use in vaccines as adjuvants (the chemicals in vaccines that enhance your immune
response to whatever you’re getting immunized against). The biggest difference between a standard
Paleo diet and the Autoimmune Protocol is where we draw the line between “yes” foods and “no” foods
in order to get more health-promoting compounds and fewer detrimental compounds in our diet. Those
who are typically quite healthy can tolerate less-optimal foods than those who aren’t. You can think of
the Autoimmune Protocol as a pickier version of the Paleo diet; it accepts only those foods that are clear
winners.

Following the AIP diet involves increasing your intake of nutrient-dense, health-promoting foods while
avoiding foods that may be triggers for your disease.

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 I N S U M M A R Y, T H E R U L E S O F W H AT T O E AT A R E :

ºº
organ meat and offal (aim for 5 times per week, the more the better)

ºº better)
fish and shellfish (wild is best, but farmed is fine) (aim for at least 3 times per week, the more the

ºº 8-14 cups per day

vegetables of all kinds, as much variety as possible and the whole rainbow, aim for

ºº
leafy green vegetables (lettuce, spinach, kale, collards, celery leaves, etc.)

ºº
colorful vegetables and fruit (red, purple, blue, yellow, orange, white)

ºº Brussels sprouts, watercress, mustard greens, etc.)

cruciferous vegetables (broccoli, cabbage, kale, turnips, arugula, cauliflower,

ºº carrots, rutabaga, turnip, acorn squash, spaghetti squash, etc.)

roots, tubers and winter quash (cassava, sweet potato, parsnip, beets, fennel,

ºº
onion family (aka alliums, onions, leek, garlic, ramps, etc.)

ºº stimulators)
sea vegetables (excluding algae like chlorella and spirulina which are immune

ºº
mushrooms (and other edible fungi)

ºº stimulators)
sea vegetables (excluding algae like chlorella and spirulina which are immune

ºº
edible fungi, like mushrooms

ºº
herbs and spices

ºº high omega-6 content unless you are eating a ton of fish)

quality meats (grass-fed, pasture-raised, wild as much as possible) (poultry in moderation due to

ºº olive, avocado, coconut, palm [not palm kernel])

quality fats (pasture-raised/grass-fed animal fats [rendered or as part of your meat], fatty fish,

ºº
fruit (keeping fructose intake between 10g and 40g daily—note that 20g is probably optimal)

ºº kefir, coconut milk yogurt,)

probiotic/fermented foods (fermented vegetables or fruit, kombucha, water kefir, coconut milk

ºº
glycine-rich foods (anything with connective tissue, joints or skin, organ meat, and bone broth)

ºº
source the best-quality ingredients you can

ºº
eat as much variety as possible

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 AIP YES FOODS
There’s a huge variety of foods to choose from within each of the major Autoimmune Protocol food groups!

ORGAN MEATS
MEAT & POULTRY FISH SHELLFISH &
blood, bone broth, bone mar-
beef, boar, bison, buffalo, anchovies, bass, bream, OTHER SEAFOOD
row, brain, chitterlings and abalone, anemone, caviar/
camel, chicken, crocodile, catfish, char, cod, eel,
natural casings (intestines), roe, clam, cockle conch, crab,
duck, emu, frog, goat, goose, haddock, hake, hali-
fries (testicles), head meat crawfish, cuttlefish,
guinea hen, kangaroo, lamb, but, herring, lamprey,
(cheek and jowl), heart, kidney, jellyfish limpet, lobster
mutton, ostrich, partridge, mackerel, mahi mahi,
lips, liver, melt (spleen), rinds mussel, octopus, oyster,
pheasant, pigeon, pork, quail, perch, pollock, salmon,
(skin), sweetbreads (thy- periwinkle, prawn, scallop,
rabbit, snake, turkey, sardines, smelt, snapper,
mus gland or pancreas), tail, sea cucumber, sea squirt, sea
turtle,venison, whale, wild tilapia, trout,tuna, many
tongue, tripe (stomach) urchin, shrimp, snail squid,
game, many other varieties other varieties
starfish, whelk

EDIBLE INSECTS
SEA VEGETABLES LEAFY GREENS HIGH-FAT FRUITS
agave worm, ant, bamboo
worm, bee larvae, cen-
aonori, arame carola, dabber- amaranth greens, arugula, avocados, black olives,
tipede,cicada, cockroach,
locks, dulse, hijiki, kombu beet greens, bok choy, coconuts, green olives
cricket dragonfly, dung
laver, mozuku, nori ogonori, borage greens, brocco-
beetle, earthworm, fly pupa,
samphire, sea grape, sea kale, li greens, cabbage, capers,
grasshopper, hornworm,
sea lettuce, wakame cardooncarrot tops, cauli-
leaves, pea leaves, poke, june bug, locust, mealworm,
flower greens, celtuce, Ceylon
pumpkin sprouts, radic- sago worm, silkworm
spinach (a.k.a. Lagos bologi,
chio, sprouts, radicchio,
waterleaf) chickweed, chicory,
radish sprouts, sculpit
Chinese mallow, chrysanthe-
(stridolo), sea beet,
mum leaves, collard greens,
sorrel, spinach, summer
cress, dandelion, endive, fat
ROSACEAE FAMILY purslane, sunflower
hen, fiddlehead, Florence
sprouts, sweet potato
(Apple Family & Stone Fruits) fennel, fluted pumpkin leaves, ALLIUMS
greens, Swiss chard,
Good King Henry, greater
tatsoi, turnip greens,
apple, apricot, cherry, crab- plantain, kohlrabi greens, abusgata, chives, elephant
water spinach, water-
apple, greengage, hawthorn, kale, komatsuna, lamb’s garlic, garlic, kurrat, leek
cress, winter purslane
loquat, medlar, nectarine, quarters, land cress lettuce, onion, pearl onion, potato
peach, pear, plum, quince, lizard’s tail, mâche, melokhia, onion, scallion, spring onion,
rowan, service tree, service- mizuna, mustard greens, napa shallot, tree onion, wild leek
berry, shipova cabbage, New Zealand spinach, (aka ramp)
orache

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MUSHROOMS & OTHER ROOTS, TUBERS & CRUCIFEROUS
OTHER FRUITS
EDIBLE FUNGI WINTER SQUASH VEGETABLES
& VEGETABLES
Beech mushroom (aka shimeji), acorn squash, arracacha, arugula (also known as
acerola, artichokes,
boletus, many varieties, button arrowroot, bamboo shoot, rocket), bok choy brocco-
asparagus, bananas,
mushrooms, many varieties beet root, boniato, burdock, li, broccoflower, broccoli
bitter melon (aka bitter
(includes portabella and cremi- butternut squash, calabaza, romanesco, Brussels sprouts
gourd), canary melon,
ni), chanterelle, many varieties carrot, cassava (aka tapio- cabbage, canola (also known
cantaloupes, capers, celery,
field blewit, gypsy mushroom, ca, yuca), celeriac, Chinese as rapeseed) cauliflower,
Christmas melon, cucum-
kefir (includes both yeast and artichoke daikon, delicata Chinese broccoli, collard
bers, dates, dragonfruit,
probiotic bacteria), king trumpet squash (aka peanut squash), greens, daikon field pepper-
durian, figs, guava, hon-
mushroom, kombucha (includes earthnut pea, Georgia candy weed, flowering cabbage
eydew melons, jackfruit,
both yeast and probiotic bacteria), roaster, giraumon, gold (or garden cress, horseradish,
kiwis, kumquat, longan,
lion’s mane mushroom, maitake, golden) nugget squash, heart kale, kohlrabi, komatsuna,
lychee, mangoes, musk-
matsutake, morel, many varieties of gold squash, horseradish land cress, maca, mizuna,
melon, nopal, okra,
oyster mushroom, many varieties hubbard squash, Jarrah- mustard, radishes, rapini
papayas, passion fruit,
saffron milk cap shiitake (aka oak dale pumpkin, Jerusalem (also known as broccoli
pattypan squash, pawpaw,
mushroom), snow fungus, Sparas- artichoke, jicama, kabocha, rabe), rutabaga tatsoi,
persimmon, pineapples
sis crispa, straw mushroom, kohlrabi, lotus root, maca, turnips wasabi, watercress,
plantains, pomegranates,
sweet tooth fungus (aka hedge- parsnip, pignut, prairie wild broccoli
rambutan, rhubarb,
hog mushroom), tree ear fungus turnip, pumpkin, radish
soursop, star fruit (caram-
truffle, many varieties winter rutabaga, spaghetti squash,
bola), watermelons, winter
mushroom (aka enokitake), yeast swede, sweet potato, taro,
melon, yellow summer
(baker’s, brewer’s, nutritional) tiger nut turnip, wasabi,
squash, zucchini (aka
water chestnut, winter
courgette)
squash, many varieties,
yacón, yam

BERRIES CITRUS FRUIT

FERMENTED FOODS
NATURAL
açaí, bearberry, bilberry, black- amanatsu, blood orange, SUGARS**
beet and other vegetable
berry, blueberry, cloudberry, Buddha’s hand, cam sành, blackstrap molasses, date
kvasses, coconut milk
cranberry, crowberry, currant, citron, clementine, fernan- sugar, coconut sugar or
kefir or yogurt, kombucha
elderberry, falberry, gooseberry, dina, grapefruit (many vari- nectar, honey, lucuma
raw, unpasteurized, lac-
grape, hackberry, huckleberry, eties) kaffir lime, key lime, powder, maple syrup or
tofermented vegetables
lingonberry, loganberry,mulberry, kinnow, kiyomi, kumquat, sugar, palm sugar or nectar
(kimchi, beets, carrots,
muscadine, nannyberry, Oregon lemon (many varieties) lime unrefined cane sugar
pickles) raw, unpasteurized,
grape, raspberry, salmonber- (many varieties) limetta,
lactofermented fruits (green ** consume in moderation
ry, sea buckthornstrawberry, mandarin, Meyer lemon,
papaya, chutneys) raw, un- and only occasionally,
strawberry tree, thimbleberry, orange (many varieties)
pasteurized, lactofermented honey and blackstrap
wineberry orangelo, oroblanco,
condiments (relishes, salsas) molasses are the best
pomelo, pompia, ponk-
raw, unpasteurized choices
an, rangpur, shonan gold,
sauerkraut, water kefir
sudachi, tangelo, tangerine,
tangor, ugli, yuzu

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HEALTHY FATS* MINERALS** BEVERAGES GUT HEALTH
SUPERFOODS
avocado oil, coconut oil, lard, Celtic sea salt, Himalayan beet and other vegetable,
leaf lard, olive oil, palm oil, palm pink salt, sea vegetable kvasses, carbonated or spar- vegetables & fruit (high
shortening, poultry fat, red palm powder (or salt), sel gris, kling water, coconut milk fiber and phytochemical),
oil, salo, schmaltz, strutto, tallow truffle salt (emulsifier-free), coconut cruciferous vegetables,
ideally cold-pressed, unrefined, ** consume in moderation milk kefir, coconut water, mushrooms, roots and
*
organic, and ethically sourced for kombucha, lemon or lime tubers, alliums, leafy
plant oils, and grass-fed or juice, mineral water, soda greens, apple family,
pasture-raised for animal fats water, tea, green, black, or citrus, berries, extra virgin
white (in moderation), tea, olive oil, fish, shellfish,
herbal (including chamomile, honey (in moderation)
chicory, cinnamon, citrus and other bee products,
rind, clove, dandelion root, fermented foods, edible
dried fruit, ginger, Greek insects, green, black and
mountain, hibiscus, white tea, bone broth
honeybush, lavender, lemon
FRESH HERBS & SAFE SPICES verbena, marshmallow root,
milk thistle, mint, olive leaf,
asafetida (check ingredients), balm (lemon balm), basil
rose hip, rooibos, sage, sea
leaves (sweet), bay leaves (laurel leaves), chamomile, buckthorn, soursop leaf,
chervil, chives, cilantro (coriander leaf), cinnamon/cassia, turmeric, and yerba mate)
cloves, curry leaves, dill weed, fennel leaf, galangal, vegetable (green) juices and
garlic, ginger, horseradish (check ingredients for horse- green smoothies (in modera-
radish sauce), kaffir lime leaves, lavender, lemon balm, tion), water, water kefir
lemongrass, mace, marjoram leaf, mint (peppermint,
spearmint, etc.), lemongrass, onion powder, oregano,
parsley, perilla leaves (aka beefsteak leaves), rosemary,
saffron, sage, savory, tarragon, thyme, turmeric,
vanilla bean

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 What Foods Do I Avoid?
As you adopt the Autoimmune Protocol, your food choices become focused on consuming the nutrients
to support healing—foods that provide everything your body needs to stop attacking itself, repair dam-
aged tissues, and get healthy again: proteins, carbohydrates, and fats to sustain a normal metabolism,
build new tissue, and produce hormones, important proteins, and signaling molecules; fiber to support a
healthy and diverse gut microbiome; and the full range of fat-soluble vitamins, water-soluble vitamins,
minerals, antioxidants and other micronutrients to get rid of inflammation, regulate the immune
system, and support the normal functioning of all the body’s systems.

However, the AIP diet goes beyond making sure that our bodies have the resources they need to be
healthy to also omit problematic foods—meaning any food that has the capacity to undermine our
health, whether by increasing inflammation, damaging the gut, negatively affecting hormones, or
causing other problems. A healthy diet isn’t just about eating more of the good; it’s also about avoiding
the bad.

Some foods are inherently inflammatory. It’s actually quite surprising just how many different ways
foods can cause inflammation. Processed foods, fast food, foods made with processed “vegetable” oils,
grains, legumes, nuts and seeds are all high in omega-6 fatty acids, which control cell signaling that
turns on inflammation.

Both high blood sugar and high insulin levels in the blood propel inflammation, so
any food that is high in refined carbohydrates, sugars, and starches that hit the blood-
stream quickly (owing to the absence of compounds in the food that slow the digestion
of carbohydrates, such as fiber) is inflammatory.

These foods also negatively impact many other

hormones, thanks to all the effects that insulin
has in the body. Insulin is a hormone that affects
many other systems in the human body, and having
insulin in the happy-medium range is critical for
health. Excess refined carbohydrates also negative-
ly impact two other important hormones: leptin
and ghrelin. These hormones help control our ap-
petite, metabolism, and immune systems. Okay, so
there go processed foods, fast food, and junk food.
But then, those foods were already on the blacklist
because they don’t possess any nutritionally re-
deeming properties. What’s less commonly known

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 is that many foods considered to be healthy, like multigrain bread and low-fat dairy products, also spike
blood sugar and insulin levels.

Several compounds found in grains (even whole grains), legumes, and nightshades are inflammatory.
Compounds called agglutinins (particularly wheat germ agglutinin, kidney bean lectin, soybean lectin,
tomato lectin, and peanut lectin) and glycoalkaloids (found in nightshades such as tomatoes, potatoes,
eggplants, and peppers) are such potent inducers of inflammation and stimulators of the immune system
that several of these compounds have been investigated for use in chemotherapy or for use in vaccines
as adjuvants, chemicals added to vaccines to ramp up the immune system. They’re a necessary aspect of
how vaccines work, but not a desirable property of food!

Some foods are inherently damaging to the gut, usually because they either harm the
beneficial microorganisms that live in the digestive tract or damage or alter the cells
that form the gut barrier, whose job is to transport nutrients to the bloodstream
while stopping everything else from getting in.

The microorganisms that live in our gut are essential to our health. They help us digest food, regulate
the gut barrier, and regulate our immune system. A healthy diversity of the right kinds of microor-
ganisms in the gut is one of the most fundamental aspects of good health. Beyond eating plenty of
fiber, phytochemicals, and omega-3 fats to support their growth, it’s also important to avoid foods that
promote the growth of the wrong kinds of bacteria. Grains, dairy, legumes, nightshades, and alcohol are
all known to contain compounds that can hinder the growth of
beneficial strains of bacteria while supporting the growth of un-
desirable strains of bacteria, like E. coli. Additionally, pesticides
including glyphosate (the active ingredient in Roundup) skew
the microbial balance in the gut towards undesirable strains, an
argument for choosing organic whenever possible.

There are two main ways foods directly damage the gut barrier:
by adversely affecting the health of the cells that form the gut
barrier or by interfering with how those cells bond together.
Both of these cause the barrier to become permeable, or “leaky”
(hence “leaky gut syndrome,” the umbrella term for chronic dis-
eases associated with this problem). Many compounds that are
supposed to stay inside the gut (like toxins, waste products, and
even otherwise beneficial microorganisms) are able to pass into
the body, where they can stimulate the immune system. Grains,
legumes, dairy, nuts, seeds, nightshades, alcohol, non-nutritive
sweeteners, and emulsifiers all contain substances that increase
the permeability of the gut either directly, by damaging the cells

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90 by Dr. Sarah Ballantyne, PhD
 that form the gut barrier or opening up the bonds between
them, or indirectly, by feeding the wrong kinds of micro-
organisms in the gut or by stimulating intestinal inflamma-
tion. These harmful substances include prolamins (like
gluten) and agglutinins, digestive enzyme inhibitors,
glycoalkaloids, and phytic acid. NSAID medications also
negatively impact gut barrier function.

Gluten-containing grains are particularly problematic foods

thanks to gluten’s direct effect on gut barrier integrity, but
also because antibody formation against gluten peptides
is extremely common in autoimmune disease. And, there
are similar enough proteins in other grains, dairy products,
some legumes and pseudograins that antibodies against
gluten also recognize proteins in these foods, a process
called gluten cross-reactivity. The most common gluten cross-reactors are also eliminated on the AIP.  

A handful of foods are additionally problematic because of their impact on hormones. This includes
coffee (impacting cortisol) and stevia (an endocrine disruptor, impacting testosterone and progesterone).
Other foods simply facilitate inflammation, such as egg whites, which contain a compound called
lysozyme that acts as a carrier molecule for other proteins (food proteins, bacterial proteins) to get
inside the body and interact with the immune system.

Finally, some foods are only problematic in large quantities. Salt (it’s best to always consume unrefined
sea salt because it contains dozens of trace minerals) should be limited to 1 to 2 heaping teaspoons per
day (equating to 5-6 grams of sodium per day). Fructose consumption (even from fresh fruit) should be
limited to 40 grams daily, and it’s best to aim for 10 to 25 grams daily. Tea is beneficial to the microbiome,
but it does still contain caffeine, so its consumption should be limited to the morning hours and
attention should be paid to its effect on sleep quality. Honey and blackstrap molasses are superfood
sweeteners (honey because it benefits the microbiome, and blackstrap molasses because it’s so crazy
nutrient-dense), yet all natural sugars should only be consumed in moderation, keeping intake to less
than 10% of total calories.

This may be an oversimplification, but we can lump together all the health-promoting nutrients in foods
as “Good Stuff” and all the health-undermining compounds in foods as “Bad Stuff.” When evaluating the
merits of an individual food, we can weigh how much “Good Stuff” is in that food versus how much “Bad
Stuff”. Some foods have tons of Good Stuff and no Bad Stuff—these are the definite “yes” foods! We can
eat plenty of them with no guilt. Other foods have tons of Bad Stuff and very little Good Stuff—these are
the definite “no” foods and should be avoided the vast majority of the time.

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 If you’re interested to dig into the scientific details of these eliminations, read The Paleo Approach by
Dr. Sarah Ballantyne, PhD .

R E M O V E T H E F O L L O W I N G F R O M YO U R D I E T:

ºº Legumes
Grains

ºº Pseudograins
ºº Dairy
ºº Refined and processed sugars and oils
ºº Eggs (especially the whites)
ºº Nuts
ºº
ºº
Seeds (including cocoa, coffee and seed-based spices)

ºº peppers, cayenne, red pepper, tomatillos, goji berries etc. and spices derived from
Nightshades (potatoes [sweet potatoes are fine], tomatoes, eggplants, sweet and hot

peppers, including paprika)

ºº Alcohol
Potential gluten cross-reactive foods

ºº Nsaids (like aspirin or ibuprofen)

ºº
ºº
Non-nutritive sweeteners (yes, all of them, even stevia)

ºº and other food additives

Emulsifiers, thickeners, food dyes, processed food chemicals,

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 Food Intolerances and Autoimmune Disease
Because increased intestinal permeability, gut dysbiosis and immune dysfunction go hand-in-hand
with autoimmune disease, people with autoimmune disease are more likely to test positive on IgG food
intolerance panels than healthy people.

One study evaluated the level of IgG antibody production in autoimmune disease sufferers compared to
healthy controls and found that autoimmune disease sufferers produce double and up to 10X more IgG
antibodies against foods than healthy people. The authors identified dairy products (both cow and goat),
rice, almonds and egg whites as being common intolerances for people with autoimmune disease.

60

50 AUTOIMMUNE

CONTROLS
IgG U/ml

40

30

20

10

CASEIN COW MILK GOAT MILK RICE ALMONDS EGG WHITE

Adapted from Coucke F. “Food intolerance in patients with manifest autoimmunity. Observational study.” Autoimmun Rev. 2018
Nov;17(11):1078-1080. doi: 10.1016/j.autrev.2018.05.011.

Another study compared the frequency of IgG food intolerance in Inflammatory Bowel Disease sufferers
compared to healthy controls. The following is a summary of the paper’s positive findings, those foods
for whom Crohn’s disease sufferers had a high likelihood of intolerance compared to healthy controls
out of the 88 foods tested.

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 FOOD % Crohn’s disease % Healthy controls
with IgG AbS with IgG Abs

Almond 16 0

Buckwheat 42 2

Corn 67 2

Lima bean 14 0

Oat 45 2

Peanut 13 0

Pecan 38 0

Pinto bean 20 4

Rice 34 0

Sesame 7 0

Soy 22 0

Sunflower seed 11 0

Walnut 7 0

Clam 12 0

Alfalfa 27 2

Asparagus 13 0

Avocado 20 0

Beets 17 0

Broccoli 17 0

Cabbage 48 6

Carrot 12 0

Celery 47 0

Cucumber 17 2

Green pepper 26 2

Lettuce 44 2

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 FOOD % Crohn’s disease % Healthy controls
with IgG AbS with IgG Abs

Onion 22 2

Potato, white 20 0

Spinach 23 0

Tomato 26 0

Grape 19 2

Grapefruit 33 0

Orange 16 0

Yeast 53 2

Cane sugar 52 0

This list of foods should not be used as a definitive guide for eliminations for IBD. First of all, this is one
study in one group of patients. The ulcerative colitis patients studied did not show the same high rates
of food intolerance as Crohn’s disease, so this is likely not a definitive list that can be applied broadly
to all autoimmune diseases. Additionally, whether or not eliminating these foods benefits IBD suffer-
ers was beyond the scope of this study. The authors are simply making the case that food intolerance
is more common in IBD.

What we can do with this data is look at overall trends to infer which types of foods are more likely
to be problematic (grains, legumes, nightshades, yeast, cane sugar, nuts and seeds) whereas others are
less likely (meat, poultry, fish, shellfish, fruits) and compare to other studies that may help to round
out this information. For example, in another study of people with unexplained gastrointestinal
symptoms, something that is incredibly common among autoimmune disease sufferers, the most
common IgG food sensitivities affecting the majority of study participants were wheat, dairy, whole
egg, yeast and cashew nut. Other common food sensitivities, affecting at least a quarter of study
participants were peas, almonds and barley. In yet another study of people with unexplained allergy
symptoms, also common among autoimmune disease sufferers, the most frequently occurring IgG
food intolerances were yeast, wheat, red kidney bean, pea, corn, egg white, barley, cow’s milk and
pistachio.

What does this tell us? The foods that are eliminated on the Autoimmune Protocol are also frequent
flyers when it comes to food intolerance in at-risk populations.

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 Testing for Allergy and Intolerance
There are ways that we can negatively react to foods that we
currently don’t have the capacity to test for, meaning that you can be
intolerant to a food even if your body does not make antibodies against
that food. This is why elimination and challenge is considered the gold
standard for identifying food intolerances. The Autoimmune Protocol is, at its heart,
a sophisticated elimination and challenge protocol, cutting out those foods which have
the highest likelihood of being problematic for people with autoimmune disease, while
focusing on nutrient-dense healing foods and healthy lifestyle.

Food allergy and intolerance testing can be helpful in troubleshooting however, because
continuing to eat foods (or be environmentally exposed to substances) you have developed
an allergy, intolerance, or sensitivity to can hinder healing. This can be done with a blood
test that looks for IgE and IgG antibodies (and rarely, but sometimes IgA and IgM antibod-
ies) against various food antigens. Panels can include anywhere between 50 and 500 dif-
ferent foods. You typically have to have eaten the food within the previous month in order
for it to show up as a positive if you are intolerant (so you can’t necessarily believe a nega-
tive result if you haven’t eaten that food in a while). These tests can be an excellent way to
expedite the process of determining whether additional foods need to be eliminated.

Note that IgG and IgE food allergy/intolerance panels do have a fairly high false positive
(10%) and false negative (30%) rates. This is actually about the same as skin prick tests for
allergies, which is why allergists will often follow up testing with an elimination diet and
food antigen challenge. It is recommended to discuss test results with a healthcare profes-
sional and follow up with an elimination and challenge protocol.

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 FOODS TO AVOID

PSEUDOGRAINS
GRAINS
GLUTEN CROSS- Amaranth, buckwheat,
barley, corn, durum, fonio, Job’s
REACTIVE FOODS chia, and quinoa.
tears, kamut, millet, oats, rice,
rye, sorghum, spelt, teff, tritica- amaranth, corn, dairy proteins (casein,
le, wheat (all varieties, including casomorphin, butyrophilin, whey),
einkorn and semolina), and wild millet, oats, potatoes, quinoa, rice, sor-
rice. Also avoid wheat grass, barley ghum (Note: instant coffee and brew-
grass, oat grass, spelt grass, bran er’s/baker’s/nutritional yeast have
and any other product made from been identified as gluten cross-reac- DAIRY
any part of the grain plant. tors in one study but it is postulated
Butter, butter oil, buttermilk,
that this is attributable to common
cheese, cottage cheese, cream, curds,
gluten contamination of these foods
dairy-protein isolates, ghee, heavy
rather than inherent cross-reactive
cream, ice cream, kefir, milk, sour
proteins. Look for options that specify
cream, whey, whey protein isolate,
GLUTEN gluten-free.)
whipping cream, and yogurt.
barley, rye, wheat, and foods
derived from these ingredients.

LEGUMES NIGHTSHADES OR PROCESSED FOOD

Adzuki beans, black beans, black- SPICES DERIVED FROM CHEMICALS AND
eyed peas, butter beans, calico NIGHTSHADES INGREDIENTS
beans, cannellini beans, chickpeas
Ashwagandha, bell peppers (aka sweet Acrylamides, artificial food color,
(aka garbanzo beans), fava beans
peppers), cape gooseberries (ground artificial and natural flavors, auto-
(aka broad beans), great Northern
cherries, not to be confused with lyzed protein, brominated vegetable
beans, Italian beans, kidney beans,
regular cherries, which are okay), oil, emulsifiers (carrageenan, cellulose
lentils, lima beans, mung beans,
cayenne peppers, eggplant, garden gum, gellan gum, guar gum, lecithin,
navy beans, pinto beans, peanuts,
huckleberries (not to be confused xanthan gum), hydrolyzed vegetable
peas, runner beans, split peas,
with regular huckleberries, which are protein, monosodium glutamate, ni-
soybeans (including edamame, tofu,
okay), goji berries (aka wolfberries), trates or nitrites (naturally occurring
tempeh, other soy products, such as
hot peppers (chili peppers and are okay), olestra, phosphoric acid,
soy protein, and soy isolates, such
chili-based spices), naranjillas, paprika, propylene glycol, textured vegetable
as soy lecithin), tamarind. Also
pepinos, pimentos, potatoes (sweet protein, trans fats (partially hydro-
avoid legume sprouts, however
potatoes are okay), red pepper, genated vegetable oil, hydrogenated
other legume plant parts (leaves
tamarillos, tomatillos, and tomatoes. oil), yeast extract, and any ingredient
as in rooibos tea or pea leaves, or
(Note: Some curry powders contain- with a chemical name that you don’t
pods as in tamarind paste or carob nightshade ingredients.) recognize
powder) are okay.

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 NUTS SEEDS

Almonds, Brazil nuts, cashews, chest- Cacao, chia, coffee, flax, hemp, poppy,
nuts, hazelnuts, macadamia nuts, pumpkin, sesame, and sunflower seeds,
pecans, pine nuts, pistachios, and wal- and any products derived from these
EGGS
nuts, and any products derived from seeds.
these nuts. (Coconut is an exception (egg yolks may be tolerated)
and may be consumed in moderation.)

A L GA E
Spirulina and chlorella.

SPICES DERIVED SPICES DERIVED FROM

FROM SEEDS BERRIES AND FRUITS

Allspice, star anise, caraway, carda- Anise, annatto, black caraway (aka
mom, juniper, pepper (derived from Russian caraway, black cumin), celery
black, green, pink, or white pepper- seed, coriander, cumin, dill, fennel,
corns; note that red pepper is a night- fenugreek, mustard, and nutmeg.
SUGAR ALCOHOLS
shade) and sumac.
Erythritol, mannitol, sorbitol,
and xylitol. (Naturally occurring
sugar alcohols found in whole
foods like fruit are okay.)
SLENDA

PROBLEMATIC ADDED
SUGARS

Agave, agave nectar, barley malt, NONNUTRITIVE

ALCOHOL
barley malt syrup, brown rice SWEETENERS
syrup, caramel, chicory root sugar, (the small amount in kombucha,
Acesulfame potassium, aspartame, monk fresh fruit, or extracts is okay.)
corn sweetener, corn syrup, corn
fruit extract, neotame, saccharin, stevia,
syrup solids, crystalline fructose,
and sucralose.
dextrin, dextrose, diastatic malt ,
fructose, fruit juice, galactose,
glucose, glucose solids, golden syrup,
high-fructose corn syrup, inulin,
invert sugar, jaggery, lactose, malt
syrup, maltodextrin, maltose, monk
fruit (luo han guo), panela, panocha, re-
fined sugar, rice bran syrup, rice syrup,
saccharose, sorghum syrup, sucrose,
syrup, treacle, and yacon syrup.

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 PALEO PRINCIPLES 281

READING LABELS
READING LABELS Trying to figure out whether a product is Paleo-friendly?
It helps to know the many aliases that some pervasive foods go by.

Gluten in Foods
Avoiding gluten takes some effort. Ingredients derived from wheat and other gluten-
containing grains are found in a vast array of packaged and manufactured foods, but also
in some foods not normally considered to be processed. The following list includes some of
these hidden—and not-so-hidden—sources of gluten.
Asian rice paper croutons gravies nutritional and herbal soy sauce (unless labeled
supplements wheat-free)
atta flour dinkle (spelt) hydrolyzed wheat gluten
oats spelt
bacon (check durum wheat hydrolyzed wheat protein
ingredients) panko (bread crumbs) spice mixes (often
einkorn ice cream
contain wheat as an
barley (may contain flour as an pilafs (containing orzo)
emmer wheat anticaking agent, filler,
anticrystallizing agent)
barley grass prepared foods or thickening agent)
farina
imitation fish
barley malt processed cereals (often starch
farro (called emmer
kamut contain barley malt)
beer (unless gluten-free) wheat except in Italy) stuffings
lunch meats rye
bleached or unbleached food starch syrups
flour maida (Indian wheat salad dressings
French fries thickeners
flour)
bran sauces
fu (a dried form of triticale
malt
bread flour gluten) seitan
wheat
malt vinegar
breading gliadin self-basting poultry
wheat bran
marinades
brewer’s yeast glues used on some semolina
wheat germ
envelopes, stamps, and matzah (aka matso)
bulgur soup bases and bouillon
labels wheat starch
medications (prescription
coating mixes soy or rice drinks
gluten peptides or over-the-counter) wheatgrass
(barley malt or malt
communion wafers
glutenin mir (a wheat and rye enzymes may be used
condiments cross) during manufacturing)
graham
couscous

COMMON SOURCES OF GLUTEN/WHEAT CONTAMINATION: Gluten Cross-Reactors

• art supplies: paint, clay, glue, and play dough (can be Some foods have a higher likelihood of cross-reacting with
transferred to the mouth if hands aren’t washed) gluten. The antibodies the body makes against gluten
• flour dust recognize similar proteins in these foods, so the body sees
these foods and gluten as being one and the same. While
• foods sold in bulk (often contaminated by scoops used in
other bins and by flour dust)
having a gluten sensitivity doesn’t automatically mean that
you are sensitive to all or any of these foods, it’s prudent to
• grills, pans, cutting boards, utensils, toasters and other
be cautious of them:
appliances, and oils that have been used for preparing foods
containing gluten

• household products (may be transferred to the lips and

ingested) brewer’s/baker’s/ corn dairy proteins
nutritional yeast (casein, casomorphin,
• knives (double-dipping knives into food spreads after
butyrophilin, whey)
spreading on bread can leave behind gluten-containing crumbs)

• millet, white rice flour, buckwheat flour, sorghum flour, and

soy flour (commonly contaminated)
instant coffee oats millet
• personal care products, especially shampoos (may be
transferred to the lips and ingested)

• powder coating inside rubber gloves (may be derived from

wheat)

• waxes or resins on fruits and vegetables potatoes rice sorghum

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Corn in Foods
Ingredients derived from corn are found in the vast majority of packaged and manufactured
foods. If you are very sensitive to corn-derived products, avoiding these pervasive ingredients
can be overwhelming. However, avoiding processed foods in general will make a huge difference.
You may or may not need to go to the extent of avoiding all traces of corn-derived ingredients
(in medications, for example); however, being aware of where corn exposure may be sneaking
into your life will help you identify whether it is a problem. The following list includes some
hidden—and not-so-hidden—sources of corn.

acetic acid cornmeal glutamate methyl glucose sodium starch glycolate

alcohol cornstarch gluten methyl glucoside sodium stearyl

fumarate
alpha-tocopherol croscarmellose sodium gluten feed/meal methylcellulose
sorbate
artificial flavorings crystalline dextrose glycerides microcrystalline
cellulose sorbic acid
artificial sweeteners crystalline fructose glycerin
modified cellulose gum sorbitan
ascorbates cyclodextrin glycerol
modified cornstarch sorbitan monooleate
ascorbic acid DATUM (a dough golden syrup
conditioner) modified food starch sorbitan trioleate
aspartame grits
decyl glucoside molasses (corn syrup sorbitol
astaxanthin hominy
may be present)
decyl polyglucose sorghum (syrup and/
baking powder honey
mono- and diglycerides or grain may be mixed
dextrin
barley malt hydrolyzed corn with corn)
monosodium glutamate
dextrose (such as
bleached flour hydrolyzed corn protein (MSG) Splenda (artificial
monohydrate or
blended sugar hydrolyzed vegetable sweetener)
anhydrous; also found in natural flavorings
IV solutions) protein starch
brown sugar olestra/Olean
D-gluconic acid hydroxypropyl stearic acid
calcium citrate polenta
methylcellulose
calcium fumarate distilled white vinegar stearyls
polydextrose
hydroxypropyl
calcium gluconate drying agents sucralose (artificial
methylcellulose polylactic acid (PLA)
sweetener)
calcium lactate erythorbic acid phthalate (HPMCP)
polysorbates (such as
sucrose
calcium magnesium erythritol inositol Polysorbate 80)
acetate (CMA) sugar
ethanol invert syrup or sugar polyvinyl acetate
calcium stearate talc
ethocel 20 iodized salt potassium citrate
calcium stearoyl threonine
ethyl acetate lactate potassium fumarate
lactylate tocopherol (vitamin E)
ethyl alcohol lactic acid potassium gluconate
caramel and caramel treacle
ethyl lactate lauryl glucoside powdered sugar
color
triethyl citrate
ethyl maltol lecithin pregelatinized starch
carboxymethylcellulose
unmodified starch
sodium ethylcellulose linoleic acid propionic acid
vanilla, natural flavoring
cellulose, methyl ethylene lysine propylene glycol
vanilla, pure or extract
cellulose, Fibersol-2 magnesium fumarate propylene glycol
microcrystalline monostearate vanillin
flavorings maize
cellulose, powdered saccharin vinegar, distilled white
food starch malic acid
cetearyl glucoside salt (iodized) vinyl acetate
fructose malonic acid
choline chloride semolina (unless from vitamin C
fruit juice concentrate malt
wheat)
citric acid vitamin E
fumaric acid malt extract
simethicone
citrus cloud emulsion vitamin supplements
germ/germ meal malt syrup from corn
(CCS) sodium
xanthan gum
gluconate maltitol carboxymethylcellulose
cocoglycerides
xylitol
gluconic acid maltodextrin sodium citrate
confectioners’ sugar
yeast
glucono delta-lactone maltol sodium erythorbate
corn oil
zea mays
gluconolactone maltose sodium fumarate
corn sugar
zein
glucosamine mannitol sodium lactate
corn sweetener
glucose margarine
corn syrup
glucose syrup (also methyl gluceth
corn syrup solids
found in IV solutions)

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Soy in Foods POTENTIALLY CROSS-CONTAMINATED FOODS

MUST BE LABELED:

Soy is another ingredient that has permeated “produced on “produced in a

the food supply. Soy lecithin and soy protein “MAY
shared equipment facility that also
CONTAIN SOY”
are especially common ingredients in packaged with soy” processes soy”

foods. The following list includes foods and

ingredients that are derived from soy:

bean curd soy lecithin PRODUCTS THAT COMMONLY CONTAIN SOY:

bean sprouts soy meal Asian cuisine (Chinese, Korean, meat products with fillers;
chocolate (soy lecithin may be soy nuts Japanese, Thai) for example, burgers and
used in manufacturing) sausages
soy pasta baked goods
edamame (fresh soybeans) nutrition bars
soy protein (concentrate, baking mixes
hydrolyzed soy protein (HSP) hydrolyzed, isolate) nutrition supplements
bouillon cubes
kinako soy sauce (vitamins)
candy
miso (fermented soybean soy sprouts peanut butter and peanut
cereal butter substitutes
paste)
soy yogurt
chicken (raw or cooked) protein powders
mono- and diglycerides
soya processed with chicken broth
monosodium glutamate (MSG) sauces, gravies, and soups
soybean (curds, granules) chicken broth
natto smoothies
soybean oil
deli meats
nimame vegetable broth
soymilk
energy bars
okara vegetarian meat substitutes
tamari
imitation dairy foods, such as (veggie burgers, imitation
shoyu
tempeh soymilk, vegan cheese, and chicken patties, imitation lunch
soy albumin vegan ice cream
teriyaki sauce meats, imitation bacon bits)
soy cheese infant formula
textured vegetable protein waxes or horticultural oils on
soy fiber (TVP) margarine fruits

soy flour tofu (dofu, kori-dofu)

mayonnaise
soy grits yuba

soy ice cream

Sugar in Foods
When reading food labels, it is helpful to know how to decipher which ingredients are sugar.
While most of them are refined, some are unrefined (which typically means that the sugar
retains some minerals). Paleo is not a sugar-free diet, but added sugars should be kept to a
minimum (less than 10 percent of total calories), and natural sugars should be reserved for
occasional treats. It is common for manufactured products to contain more than one form of
sugar. The following ingredients are all forms of sugar:
agave corn syrup galactose maple syrup saccharose

agave nectar corn syrup solids glucose molasses sorghum

barley malt crystalline fructose glucose solids monk fruit (luo han guo) sorghum syrup

barley malt syrup date sugar golden syrup muscovado sugar sucanat

beet sugar dehydrated cane juice high-fructose corn syrup palm sugar sucrose

brown rice syrup demerara sugar honey panela syrup

brown sugar dextrin inulin panocha treacle

cane crystals dextrose invert sugar rapadura turbinado sugar

cane juice diastatic malt jaggery raw cane sugar yacon syrup

cane sugar evaporated cane juice lactose raw sugar

caramel fructose malt syrup refined sugar

coconut sugar fruit juice maltodextrin rice bran syrup

corn sweetener fruit juice concentrate maltose rice syrup

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Dairy in Foods
Dairy ingredients are more and more commonly used in manufactured and
packaged foods. The following ingredients indicate the presence of milk protein:

Milk: acidophilus milk, buttermilk, buttermilk Half & half MAY CONTAIN MILK:
blend, buttermilk solids, cultured milk, Caramel flavoring
Hydrolysates: casein hydrolysate, milk
condensed milk, dried milk, dry milk solids
protein hydrolysate, protein hydrolysate, Flavoring
(DMS), evaporated milk, fat-free milk, fully
whey hydrolysate, whey protein
cream milk powder, goat’s milk, Lactaid High-protein flour
hydrolysate
milk, lactose-free milk, low-fat milk, Lactic acid
malted milk, milk derivative, milk powder, Ice cream, ice milk, sherbet
Lactic acid starter culture
milk protein, milk solids, milk solid pastes, Lactalbumin, lactalbumin phosphate
nonfat dry milk, nonfat milk, nonfat milk Natural flavoring
Lactate solids
solids, pasteurized milk, powdered milk,
sheep’s milk, skim milk, skim milk powder, Lactic yeast
sour milk, sour milk solids, sweet cream
Lactitol monohydrate
buttermilk powder, sweetened condensed
milk, sweetened condensed skim milk, Lactoglobulin “Nondairy” products may contain casein.

whole milk, 1% milk, 2% milk Lactose Foods covered by the FDA labeling

Butter: artificial butter, artificial butter laws that contain milk must be labeled
Lactulose
flavor, butter extract, butter fat, butter “contains milk”; however, prescription and
Milk fat, anhydrous milk fat
flavored oil, butter solids, dairy butter, over-the-counter medications are exempt.
natural butter, natural butter flavor, Nisin preparation
whipped butter
Nougat
Casein and caseinates: ammonium
Pudding
caseinate, calcium caseinate, hydrolyzed
casein, iron caseinate, magnesium Quark

caseinate, potassium caseinate, sodium Recaldent

caseinate, zinc caseinate
Rennet, rennet casein
Cheese: cheese flavor (artificial and
Simplesse (a fat replacer)
natural), cheese food, cottage cheese,
cream cheese, imitation cheese, vegetarian Sour cream, sour cream solids, imitation
cheeses with casein sour cream

Cream, whipped cream Whey: acid whey, cured whey, delactosed

whey, demineralized whey, hydrolyzed whey,
Curds
powdered whey, reduced mineral whey,
Custard sweet dairy whey, whey powder, whey

Dairy product solids protein, whey protein concentrate, whey

solids
Galactose
Yogurt (regular or frozen), yogurt powder
Ghee (cultured ghee may be okay)

Processed and Refined Oils

Beyond avoiding fast food, do not use any of the following oils in home cooking,
and avoid packaged foods with any of the following items on the label:

canola oil peanut oil fake butter substitutes

corn oil safflower oil butter flavor

cottonseed oil shortening nonstick cooking sprays

grapeseed oil soybean oil any oil labeled as refined

margarine sunflower oil any oil labeled as hydrogenated

palm kernel oil “vegetable” oil any oil labeled as partially

hydrogenated

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 AIP LIFESTYLE
Scientific studies into the biological mechanisms of lifestyle factors emphasize the importance to our
long-term health of regular sleep, low chronic stress, living an active lifestyle, spending time outside
and in nature, and nurturing strong social bonds. These are important not just for immune regulation,
but also gut health, hormone regulation, and both physical and mental health in general.

Another reason for focusing on both diet and lifestyle factors is that there’s a direct link between them,
meaning that making better choices in one arena will help with the other. For example, eating a high-
fiber diet and a serving of starchy carbs at dinner can help improve sleep quality. And consuming enough
omega-3 fatty acids while limiting caffeine intake is a boon to our stress responses. Conversely, our life-
style directly affects our food choices—we crave high-sugar and high-fat foods when we’re stressed or
tired, for example.

And people who get at least 7 hours of sleep every night are more likely to choose
vegetables and fruits over fast food.

In addition, how our bodies respond to diet is influenced by aspects of our lifestyle. For example, studies
show that we don’t experience the same anti-inflammatory benefits from good food choices when we’re
stressed. And one night of lost sleep is as detrimental to blood sugar regulation as six months of poor diet.

Sleep
Studies show that adults need seven to nine hours of sleep every single night. Getting enough sleep
reduces the effects of stress on our bodies and has a tremendous positive impact on our hormones, metab-
olism, and insulin sensitivity. On the other hand, shortchanging our sleep by even a small amount, even a
few times a week, can have terrible consequences on our health. The regulatory arm of our immune sys-
tems works primarily while we’re sleeping, so just plain not getting enough sleep causes inflammation.
Sleep is intricately tied to how our bodies respond to stress as well as insulin regulation—in fact, studies
show that a single night of lost sleep can harm our insulin sensitivity as much as 6 months of bad diet
does.

The importance of consistent adequate sleep cannot be underestimated. And while seven hours may seem
like a doable minimum, if you’re battling a chronic illness, chances are your body needs more than that.

The single best thing you can do to prioritize sleep is to have a regular bedtime—
a bedtime that is early enough that you can get at least eight hours of sleep (or more,
if eight hours isn’t enough for you to wake up feeling refreshed and energized).
Having a bedtime is such a simple thing, but it’s one of the hardest things for adults to implement.
Everything seems to be more important than sleep: going out with coworkers after work, watching that

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 amazing new television show, checking social media, doing the
Improving Sleep
laundry . . . But sleep must come first, not just in the initial heal-

ºº Use a light-therapy box on

ing phase of our health journeys but for the rest of our lives. Spend time outside every day.

What else can we do to ensure that we get good sleep? Spend days you don’t go outside or when
some time outside during the day and keep your indoor lighting the weather is gloomy.
dim in the evening—this helps maximize the production of
ºº and use blue-blocking glasses for
Keep lights dim in the evening
melatonin, the hormone that regulates sleep, in the evening.
Sleep in a cool, dark, quiet room. And avoid anything stimulat- the last 2-3 hours before bed.
ing (such as work, exhaustive exercise, arguments, and
ºº that is cool, quiet, and a place
Sleep in a dark environment
emotionally intense, scary, or suspenseful TV shows and
movies) in the last two hours before bed. It can also be helpful you associate with peace and rest.
to avoid evening snacking.
ºº “on schedule”
Keep mealtimes and exercise

Stress Management ºº getting enough sleep and stick

Figure out your ideal bedtime for

Stress has a direct impact on immune system function, nervous with it.
system health, and—via the gut-brain axis—gut health. Being
under chronic stress (the kind that most of us struggle with)
both increases inflammation and undermines the regulatory
functions of the immune system. Chronic stress can inhibit
digestion, encouraging the development of gut dysbiosis and
leaky gut. And chronic stress can impact our endocrine system via effects on central nervous system
function, blunting thyroid function and sex hormone production, and causing insulin resistance. Stress is
a major contributor to chronic illness, and when stress is out of control, it worsens the prognosis. When
it comes to stress management, there are two factors: stress reduction and resilience.

Reducing stress means removing things from our lives that are causing stress. Even if individual
responsibilities aren’t causing undue stress on their own, the sheer number of them on our plates may
be creating stress. Whenever you can, say no, or ask for help to reduce stress. There are as many ways to
reduce stress as there are stressed people—it’s up to you to figure out what works for you. Take a
critical look at everything you do and how it impacts your stress level, and determine where you can
make small changes (or big ones!) to reduce stress.

Resilience refers to how the body responds to stressors. This is different from
reducing stress—it’s about implementing strategies so that the stressful aspects
of your life just don’t get to you as much.
Activities that improve resilience include getting enough sleep, being physically active, meditating,
forming social bonds, connecting with nature, laughing, and playing. Making time for these things can
have a direct impact on both your health and your sense of well-being.

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 Activity
We all know that we’re supposed to exercise, but what is
much less well known is that gentle movement throughout
the day and daily weight-bearing exercise (like walking) has
a bigger impact on overall health than a sweaty session at
the gym five times per week. Yes, building muscle has all
kinds of health benefits, and including some exercise ses-
sions during the week is awesome, but when it comes to the
immune system, it’s more important to simply avoid being
sedentary. That means not sitting all day!

There are lots of ways to add movement to your day, but the
simplest strategy is to set a timer to go off every 20 minutes
during the part of the day when you typically sit (at work
and in front of the television, for most of us). Whenever the timer goes off, get up and move around for 2
minutes. You can walk around, jump rope, do some push-ups, stand and stretch, or do some yoga poses—
whatever works for you.

Managing Stress
Decrease the number and severity of stressors in your life
ºº It’s OK to ask for help.
It’s OK if you can’t do it all.

ºº
Decrease the effect that stressors have on you
ºº Take a few moments for deep breathing or stretching during the day.
Practice mindfulness for 10-15 minutes daily

ºº Maintain good posture.

ºº Find excuses to get up and move.
ºº Leave your work at work.
ºº Engage in stress-relieving activities before and after work.
ºº Have fun with hobbies, humor, and enjoying nature.
ºº Use your brain (learn a language or an instrument, puzzles, reading).
ºº Turn your brain off with active (yoga, tai chi, martial arts) or mindful meditation.
ºº Nurture yourself with small changes like music, candlelight,
ºº aromatherapy, getting a massage, using a light alarm, or a gratitude journal.
ºº thinking, and a secure social network.
Increase your resilience with humor, faith in your abilities, planning, positive

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 Getting Active
Yes, studies show that just 2 minutes of
ºº moderately-intense activity per
Aim for at least 300 minutes of
movement for every 20 minutes of sitting
week, like walking, swimming,
is all it takes.
yoga, tai chi, gardening, dancing,
Of course, you can ramp this up with a treadmill desk or bicycling, weight lifting, fitness
bicycle desk if you have access to those sorts of things. classes, and various sports.

ºº try swimming, water-exercise,

If you have limited mobility,
There are tremendous health advantages to one of the
simplest and most accessible activities out there: walk- water-therapy, chair exercise,
ing. Walking helps build muscle, improves cardiovascu- and chair aerobics.
lar health, strengthens bones, helps improve resilience
ºº are sedentary (like a desk job), take
If you have parts of your day that
to stress, improves brain health (everything from mood
to memory to cognition) and reduces the risk of prob- a 2 minute movement break every
lems like dementia, improves hormone health, and can 20 minutes.
even help us sleep better! If all you do is make time for a
ºº active desk at work (treadmill desk,
Investigate the option of an
30-minute walk every day (in addition to moving every 20
minutes throughout the day), you are doing great. desk elliptical, desk cycle).

ºº sedentary.
When it comes to exercise, more isn’t necessarily better. Take up a hobby that is not

Exhaustive, strenuous, and overly intense exercise can ac-

ºº activity.
tually undermine health by harming the immune system, Avoid strenuous, exhaustive
gut health, and hormone health.

Nature and Sunlight

Exposure to nature and sunlight has been an integral part
of human life since the very beginning of our existence.
Only relatively recently have we transitioned to indoor
lifestyles where we can go days—even weeks—without
spending substantial time in the fresh air and sun.

Ample evidence exists that time outdoors has positive ef-

fects on immune function, cardiovascular disease risk factors, and mental health. For example, spending
several hours in a forest gives an impressive boost to the immune system, including increasing natural
killer cell activity by 50%, which improves the immune system’s capacity to detect and eliminate can-
cerous cells and cells infected with viruses and parasites. When that forest trip is increased to 3 days,
research has shown that natural killer cell activity, the number of natural killer cells, and intracellular
anti-cancer protein levels remain elevated for at least 7 days after the trip is over!

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 What about those of us who only have time to sit amidst a
tree grove on our lunch breaks?

It turns out that nature has such a powerful effect

on our health that spending as little as 30 minutes
per week in a green space can reduce the rates of
high blood pressure and depression by 7% and 9%,
respectively. The more time spent in nature per
week, the lower the risk—but even short visits to
some greenery are worth it.

Another major benefit of being outside is sun exposure.

When exposed to ultraviolet light, our bodies produce vita-
min D, which plays a critical role in health (vitamin D con-
trols the expression of more than 200 genes and the proteins
regulated by those genes). The functions of vitamin D in our bodies include mineral metabolism,
immunity, regulation of inflammation, cell growth, and biorhythm activation. In addition, cells through-
out the body, including the skin and eyes, directly affect the pituitary gland and hypothalamus region of
the brain when stimulated by blue light from the sun. As a result, sun exposure (and exposure to
daylight in general) is vital for regulating our circadian rhythm, and improving sleep quality.

Connection
An often-underrated lifestyle factor that directly impacts our health is community. Connecting with
others, whether a spouse, child, friend, family member, or pet, helps regulate hormones and neurotrans-
mitters that directly impact inflammation. Genomics studies have shown that people who are socially
isolated tend to under-express genes involved in anti-inflammatory responses while over-expressing
genes involved in proinflammatory responses, which is how being socially disconnected or stressed
promotes inflammation in the body. In contrast, higher degrees of social integration, which encompasses
a person’s ties to family, friends, and the larger community, are associated with lower levels of inflam-
mation markers (including interleukin-6 and C-reactive protein).

There’s also a strong link between connection and how we respond to stress. Feeling socially connected
lowers cortisol and makes us more resilient to psychological stressors, meaning that our bodies produce
less cortisol when we’re stuck in traffic and late for a meeting. Positive social interactions reduce the
effects of chronic stress, and that leads to improved health over the long term.

There’s a practical aspect to connection as well. When we have people in our lives whom we can depend
on, we have resources to help us reduce stress and put other priorities, like getting enough physical
activity and sleep, at the top of our to-do lists. And having a companion while we tackle the job of heal-

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 ing, whether it’s a walking buddy, a friend to meet up with
at the farmers market, someone to watch the kids while
we exercise, or a family member to batch cook with on
weekends, can make all the difference.

For some people, making community a priority requires

effort and dedication. It can be easy to let social media sites
provide us with the illusion of connection without having
real, meaningful interactions with friends and family. It also
can be easy to let every other item on our to-do lists sup-
plant quality time with the people we care about. If you’re
struggling to find time for connection, think about how you
might combine social interaction with other activities, like
exercising, shopping, and even cooking.

Your lifestyle plays an important role in regulating your hormone systems, which in turn
helps regulate your immune system.
Hormone balance is critical for immune health, which is why diet change can only go so far if you aren’t
addressing lifestyle factors that may be holding you back. Making small changes to the way you exer-
cise, sleep, eat, socialize, and handle stress can reap enormous health benefits. It’s okay if your lifestyle
becomes a constant work in progress. Getting your ducks in a row (and keeping them there) takes time,
dedication, and is a constant learning process.

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 LEARN MORE

The AIP Lecture Series

The Autoimmune Protocol Lecture Series is a 6-week video- based, self-directed online course that will
teach you the scientific foundation for the diet and lifestyle tenets of the Autoimmune Protocol.
Think of this course as going to college for your health!

THE AIP LECTURE SERIES FEATURES:

ºº action steps to help you go from theory to practice
42 video lectures (totaling 16 hours!), all taught by Dr. Sarah Ballantyne, PhD

ºº dozens of printable guides

ºº daily self-discovery exercises to reinforce and refine implementation
ºº an online forum to connect with other students and ask questions
ºº guided discussions in the online forum
ºº weekly FAQ videos by Dr. Sarah Ballantyne, PhD in the online forum
ºº recommended reading for every topic
ºº interactive quizzes to test your knowledge
ºº
Click here to learn more!

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 PA R T T H R E E

Practical AIP

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 TRANSITIONING
TO THE AIP
When it comes to transitioning, there’s no one-size-fits-all
strategy that works for everybody. Some people do better
embarking on a complete diet and lifestyle overhaul from
day one. Others do best (both physically and psychologi-
cally) with a slower transition process. Neither strategy is
better or worse than the other.

The most important thing is finding what works

best for you in terms of tackling change and
sticking with it so that the AIP (or AIP plus
reintroductions) becomes your default lifestyle.

Ultimately, this boils down to maximizing compliance and sustainability.

Compliance refers to how well you can adhere to a particular protocol as prescribed, whether it’s a
diet, a medication, an exercise program, or some other intervention. In the medical and pharmaceutical
fields, compliance is seen as an indicator of not only how well a particular medication works, but also
how severe (or tolerable) the side effects are. If a drug results in extreme side effects and doesn’t work
very well, fewer people end up taking the drug as directed, resulting in low compliance. On the other
hand, if a drug works as promised and doesn’t produce many side effects, more people will take the
drug as prescribed, resulting in high compliance. When it comes to the AIP framework, the concept is
similar: compliance reflects how closely the way you eat follows the protocol. In this case, compliance
refers to how often you eat something you know isn’t good for you, will cause a negative reaction, or
will interfere with your body’s healing. For the purpose of transitioning, choosing the approach that
maximizes your compliance is critical.

Sustainability refers to the ability to be maintained at a certain rate or level. Depending on which
aspect of AIP we’re talking about, this could refer to environmental sustainability, economic sustain-
ability, individual sustainability, or many other things. In the context of implementing dietary and
lifestyle changes, though, the focus is on individual sustainability—your ability to stick with AIP (or AIP
plus reintroductions) for the long haul. In that sense, it’s important to choose a transition method that
feels manageable and sets you up for long-term success.

Ultimately, how you transition is up to you. How you handle changing your diet and lifestyle will de-
pend on a wide range of variables that are unique to your situation, including how you are eating now,

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 what your personality is like, how strong your support network is, how motivated you are to heal from
existing illnesses, how comfortable you are in the kitchen, and how accessible these changes are for you.
As long as you end up reaching your goal, there’s no right or wrong way to transition.

Make or Break a Habit in 21 Days?

Transition is about making healthy choices a habit. Unfortunately,
it’s a myth that it takes only 21 days to make or break a habit.
The vast majority of us must commit to repetitively performing
a task for a much greater length of time before that task becomes
automatic. Scientific research shows that the average length of
time it takes to form a new habit is more like 66 days, but it can take up to 254 days
before that new change we’re working on feels completely natural and easy. Being
prepared for a longer haul when it comes to creating new healthy habits is the first key
to success.

Studies have identified these five simple steps for forming a habit:
1. Decide on a goal that you would like to achieve.
2. Choose a simple action that will move you toward your goal and that
you can do on a daily basis.
3. Plan when and where you will perform your chosen action. Be consistent:
choose a time and place that you encounter every day of the week.
4. Every time you encounter that time and place, perform the action.
5. Within 10 weeks (or up to 8 months), you should find that you are
performing that action habitually without even having to think about it.
Congratulations, you’ve formed a healthy new habit!

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 THE ALL-IN CHALLENGE
The all-in challenge, whether it’s a 30-day of strict AIP mindset or simply a jump all-in on your chosen
start day approach to change, is a tried-and-true transition method. This strategy compresses both
the physical and psychological adaptations along with the more practical learning curve into one
short period.

This method expedites the healing process so most people see substantial
health improvements in a relatively short period of time (a few weeks to a few
months) that help them stay motivated to continue, while also having dealt
with the biggest practical challenges to long-term success.

Who Does This Method Work For?

Think about your personality for a minute. Are you more likely to stick with something if you approach
it as if you’re breaking a bad habit, investing plenty of up-front effort to make a change until a new habit
is solidified and the change feels effortless? Are you more likely to stick with a new dietary approach if
you see quick results? Are you more likely to have an all-or-nothing attitude and throw in the towel if
you aren’t completely on board? Are you very ill and need a rapid intervention? If you answer “yes” to
these types of questions, an all-in challenge might be right up your alley. This approach fully immers-
es you in the AIP lifestyle so that you can start forming new habits—and seeing results!—as quickly as
possible.

How to Do It
Before diving in, it’s important to take time to prepare. This often means setting up a meal plan, shop-
ping for AIP-friendly ingredients, cooking extra food to freeze for later, and organizing your support
network. When it comes to jumping in with both feet, it’s a good idea to clean out your pantry of foods
you know you won’t be eating anymore, which also helps you assess your food inventory. For example,
you might already have olive oil, vinegar, herbs, and other AIP-friendly items on hand, so you won’t
need to buy them. Decide which meals you plan to cook over the first week or so and make a shop-
ping list of all the ingredients you don’t have. This strategy ensures that you’ll be prepared during this
cold-turkey approach and lets you stock your pantry slowly over the course of a few months, buying
new items as you plan for the coming week.

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 What to Expect
Although a cold-turkey approach reduces the amount of time it takes to start feeling fantastic, it can be
a little jarring. Fortunately, there’s an advantage to forcing yourself to adjust quickly (and only once):
this approach typically results in faster, more dramatic improvements. Be warned, though, that even
when you “get the transition over with” this way, some people experience a lag while their bodies adjust
to new foods and different macronutrient ratios before they start to see improvements. However, many
others report phenomenal changes in long-standing symptoms, energy levels, mood, sleep quality, and
overall well-being within the first few days of transitioning.

At the other end of the spectrum, rapid transitions can trigger symptoms resembling Jarisch-Herx-
heimer reactions (a reaction to the endotoxin-like products that are released when harmful microorgan-
isms in the body die), though this isn’t very common and certainly isn’t permanent.

As a result of changes in gut microflora, increases in stool bulk (if your fiber intake goes up), increases
in stomach acid requirements, increases in fat intake, and/or decreases in carbohydrate intake, certain
symptoms are particularly likely in the first few days or weeks of a cold-turkey transition. Temporary
gastrointestinal issues such as bloating, looser stools, constipation, and more or less frequent bowel
movements can occur in response to gut microbiome shifts and higher fiber intake. As the stomach
adjusts to producing more acid in response to high-protein foods, fiber-rich foods, and fat, symptoms
such as heartburn, nausea, acid reflux, and belching can result.

When carbohydrate intake significantly decreases (which often happens when we stop consuming grains
and processed sugars), the “carb flu” can occur; it is characterized by symptoms such as fatigue, head-
aches, muscle cramps, brain fog, and dizziness—many of which can be relieved by drinking more water;
ensuring adequate intake of sodium, potassium, and magnesium; and upping carbohydrate intake by
incorporating more tubers, root vegetables, and fruit.

That being said, transition symptoms should be temporary and mild enough
not to cause serious alarm.
If you experience symptoms that don’t subside after the first several weeks of AIP, that interfere with
your ability to function throughout the day, or that indicate a worsening of a health condition (such as
increased pain or stiffness), talk to your doctor. You could have introduced a particular food into your
diet that isn’t a good fit for your body; for example, you may have a sensitivity to an AIP-friendly food
that you weren’t eating before.

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 Transition Guide: How to Go Cold Turkey
The key to success with an all-in challenge is to take some time in advance to prepare,
using the following suggestions:

ºº Clean out your pantry.

Study the food lists.

ºº Plan your meals.

ºº Restock your pantry.
ºº Think about snacks, on-the-go foods, and quick and easy meals.
ºº Go grocery shopping for fresh and frozen ingredients.
ºº Think about nutrient-dense foods and how to incorporate them.
ºº Evaluate your sleep.
ºº Plan some activity.
ºº Assess your stress level.
ºº Make a detailed plan for lifestyle adjustments.
ºº Pick a day and do it!
ºº

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 THE STEP-BY-STEP
APPROACH
Another absolutely acceptable method of transition is to prioritize individual aspects of the AIP
diet and implement them iteratively.

There’s no prescribed length of time that each step should take, some people
allot a week to each step while others simply move on once they feel like the
previous step is mastered (which can take days or months). The key here is not
to lose site of the end goal and keep progressing toward it.

Who Does This Method Work For?

Are you more likely to stick with something if you ease into it and make one manageable change at a
time? Can you be patient and optimistic if you don’t see immediate results? Are you transitioning along
with children or other family members who aren’t ready for a sudden, complete overhaul of their
current diet? Is the AIP your first foray into healthy eating, and is your current diet a long way off from
your goal? Is your autoimmune disease fairly stable with no immediate need to transition more quick-
ly? These situations suggest that a step-by-step approach could be better for you. The results might not
come as fast, but you’re more likely to make lasting habits and avoid feeling overwhelmed, leading to
better compliance and less risk of falling off the wagon.

How to Do It
The step-by-step approach involves implementing changes in phases and solidifying each new change
before moving on to the next one. The best way to do so is by creating a game plan for which changes
you want to make first, second, third, fourth, and so on. Different people will prioritize different chang-
es for different reasons: with autoimmune disease, eliminating gluten may be a top priority; if you know
that eating veggies is a particular challenge for you, adding a serving or two per meal might be where
you start; if you’re a junk food junky, you might begin simply with finding healthier alternatives; and if
you eat most of your meals out, simply getting into the routine of grocery shopping and cooking at home
will be your step one.

As you adopt each new step in your plan, you’ll know you’re ready to move on once you’ve adjusted to
the absence of certain familiar foods (like bread and breakfast cereal) and have found a “new normal”
in terms of what meals should look like—such as leftover meat and vegetables for breakfast instead
of milk and toast. Some steps may feel easy and you can move onto the next one in a few days. Oth-

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 ers might be tough and you find that you aren’t ready to tackle the next step for a few weeks or even
months. The key with the step-by-step approach is to never lose sight of the end goal: even if you’re
making very gradual changes, make sure you’re still progressing towards full implementation of the AIP.

What to Expect
Although some people feel better and better with each step, many won’t see major improvements—or,
in some cases, even minor improvements—until they eliminate all problem foods from their diets. For
example, if you’re sensitive to gluten and dairy, you might not notice any big differences in how you
feel until gluten and dairy are completely removed from your diet, regardless of the other changes you
make. So when choosing the step-by-step approach, it’s important to keep in mind that you can’t expect
to see substantial results until you’ve taken all the steps toward a fully AIP diet.

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 Transition Guide: Incremental Implementation
There are about a million ways to implement a step-by-step approach to transitioning to
an AIP diet. The following are suggestions to prioritize dietary changes based on the health
impact of each change:

ºº and processed and fast food).

Eliminate gut-irritating foods from your diet (at the minimum, gluten,dairy, soy

ºº
Start cooking all your meals.

ºº shellfish), some vegetables (ideally of a few different colors, including at least one
Get used to your meals consisting of some kind of protein (meat, poultry, fish, or

that is green) and maybe some fruit.

ºº
Start thinking about healthy fats.

ºº
Think about nutrient density.

ºº
Tackle additional eliminations (all grains, legumes, nightshades.)

ºº
Work on eating variety and maybe adding some new foods.

ºº
Purge your pantry.

ºº caught seafood as often as possible.

Address food quality, seeking out local, organic produce, grass-fed meat, and wild-

ºº haven’t cut out yet!)

Implement the rest of the eliminations (nuts, seeds, eggs, and anything else you

ºº
Find support and nourish connection.

ºº an active lifestyle
Don’t forget the lifestyle factors! Work on more sleep, lower stress, and

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 Know Your Currency
When people are hesitant to pursue the AIP, even knowing that they
stand to reap great benefits, it’s usually over an unwillingness to give
up a favorite food. The most frequent concern usually goes like this:
“I would start the AIP, but I can’t give up _____.”

Yes, it is a very common barrier to following the AIP, that one thing that someone just
can’t give up. It’s usually coffee or chocolate, but sometimes it’s wine or dairy or even
soda.

Here’s the thing. We think that the AIP is only worth pursuing if we complete adhere to
it 100% for months on end. Certainly, doing so is the most expedient way to heal, to
enjoy the benefits of the AIP, and get to those life-enhancing reintroductions, but it’s
not the only way to go about the AIP. So, if that one thing is keeping you from diving
into the AIP, keep it in your diet and do everything else prescribed on the AIP. If this one
compromise is what gets you to take that first step, to make all of the other amazing,
positive, healthy choices associated with your diet and lifestyle, then that is your cur-
rency. Buy in!

As for our cup of coffee, glass of wine, piece of dark chocolate, handful of nuts or
occasional fried egg: I want to emphasize that for those of us with autoimmune disease,
enjoying these in moderation while following (most of) the AIP is a better approach for
our overall health than not following it at all. Just be mindful of your improvements,
and remember to periodically reassess. If you’re not where you want to be after a few
months, consider eliminating the foods you were initially hesitant to cut out. If you are
reacting to a food that you haven’t eliminated, that could be holding back your progress
partially or completely.

So, if giving up that one thing is a non-starter for you, instead of thinking of it as a
barrier to making healthy changes, think of it as your currency. If trading keeping that
one thing in your life allows you to finally take steps towards regaining your health,
that’s a deal worth taking!

119 THE AUTOIMMUNE PROTOCOL

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 From New Flavors to New Favorites
This might be a great time to emphasize that it only takes a few weeks for our taste buds
to adapt to big shifts in our diets. Studies looking at taste adaptation to one of a low-sugar,
low-salt, or low-fat diet have shown that over the course of a few weeks (4 to 12 weeks,
depending on the study), participants develop a preference for the healthier foods they’ve
been eating. This is attributable to our taste buds becoming more sensitive. Food familiar-
ity and flavor association with positive experiences
(e.g., feeling good physically, the food tasting good,
or eating in a positive social environment) is another
key driver of food preference. Studies show that with
repeated exposure to foods that we innately dislike,
we can not only lose our aversions to those foods but
we can actually develop a preference for them. In fact,
we can learn to like new flavors after trying them as
few as four or five times. What does this mean? If you
aren’t enjoying the new healthy foods you’re adding
to your diet, don’t give up! The more of these healthy
foods you eat, the more you’ll enjoy them!

120 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 EAT
AIP CHEAT SHEET

Leafy Vegetables Roots and Mushrooms & Red meat Poultry Fish Shellfish Sea vegetables
Berries Other Fruit
tubers other edible fungi

Cruciferous Aliums Other Citrus Fermented Herbs and Healthy fats Edible insects Wild game Wild edibles
Vegetables Vegetables foods spices

AVOID BALANCED MACRONUTRIENTS:

20% to 35% 20% to 40% 20% to 50%

PROTEIN CARBOHYDRATE FA T

Trans fats Chemical Artificial colors High-fructose

additives and flavorings corn syrup
EXAMPLES OF AIP FOODS
LEAFY VEGETABLES: kale, lettuce, SEA VEGETABLES: arame,
spinach, mizuna, arugula, collards kelp, kombu, nori, wakame

CRUCIFEROUS VEGETABLES: RAW FERMENTED FOODS:

Grains Pseudograins Legumes Dairy broccoli, brussels sprouts, cabbage, pickles, sauerkraut, kombucha,
(especially (especially soy, products cauliflower, turnips, kohlrabi water kefir, apple cider vinegar
wheat, barley, peanuts, and
and rye) kidney beans)
ROOTS AND TUBERS: beets, HERBS AND SPICES: basil,
carrots, cassava, parsnips, sweet oregano, parsley, rosemary,
potatoes cinnamon, ginger, turmeric

ALLIUMS: garlic, onions, leeks HEALTHY FATS: extra-virgin

olive oil, avocado oil, coconut oil,
OTHER VEGETABLES: asparagus, pasture-raised lard, grass-fed
Processed and Refined Sugar Refined celery, artichoke, okra tallow
refined foods sugars substitutes vegetable oils
(including stevia) BERRIES: blackberries, blueberries, UNREFINED SEA SALT:
cranberries, grapes, raspberries Himalayan pink salt, Celtic sea
salt, sea vegetable salt
CITRUS: clementines, grapefruit,
lemons, limes, oranges FISH: cod, halibut, mackerel,
salmon, tuna
MUSHROOMS: button, cremini,
oyster, portabella, shiitake SHELLFISH: clams, mussels,
Eggs Nightshades Alcohol Coffee oysters, scallops, shrimp
(including OTHER FRUIT: mango, fig, apples,
white potatoes) cucumbers, melons, squash, plantain HIGH-FAT FRUIT: olives,
avocados, coconut
RED MEAT: beef, bison, lamb, pork,
rabbit GUT HEALTH SUPERFOODS:
seafood, mushrooms, veggies,
ORGAN MEAT: heart, kidney, liver, cruciferous veggies, roots &
sweetbreads, bone broth tubers, alliums, honey, tea, edible
Nuts Seeds insects, extra virgin olive oil,
POULTRY: chicken, turkey, duck,
high fiber, high polyphenol, bone
goose, pheasant
broth, fermented foods

MODERATE IMPORTANT DIETARY FACTORS

Nutrient density High fiber (lots of veggies!)
Seasonal variation High phytochemicals (lots of veggies!)
High variety Gut health superfoods
Snout-to-tail (nothing wasted) Whole, unprocessed, unrefined foods

Tea Natural Unrefined

Sugars Sea Salt

121 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CONSTRUCTING AN AIP PLATE
CONSTRUCTING AN AIP PLATE

122 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 WHAT’S IN YOUR
AIP KITCHEN
WHAT’S IN YOUR AIP KITCHEN?
Now that you have the right information When it comes to restocking your pantry,
about how to eat healthy, the next big hurdle you don’t need to go out and buy everything
is actually doing it! This means throwing out listed here in one enormous (not to mention
(or composting or donating to a food bank) expensive!) shopping trip. Instead, add a few
all the food in your home that you don’t plan items to your pantry each week, prioritizing
to eat anymore, and then restocking your those ingredients that you’ll need for the
freezer, fridge, and pantry with nutrient- meals you plan to make that week. Stocking
dense choices. a few emergency proteins and grab-and-go
snacks also makes life easier.

WHAT’S
IN THE
PANTRY

Dried herbs and

Fats: avocado oil, coconut seasonings: basil, dill,
oil, olive oil, lard, tallow marjoram, mint, oregano,
Vinegars: apple cider rosemary, sage, thyme,
vinegar, balsamic vinegar, garlic powder, onion
pear cider vinegar, red powder, cinnamon,
wine vinegar cloves, ginger, mace,
sea salt, truffle salt
Emergency proteins:
canned haddock, Flavorings: anchovies,
mackerel, oysters, salmon, coconut aminos, fish sauce
sardines, shrimp, tuna (check ingredients for
“ no ” foods), wasabi (check
Pickled staples: artichoke ingredients for “ no ” foods)
hearts, olives, horseradish
(check ingredients for Dried fruits: apples,
“ no ” foods) bananas, coconut, dates,
mangoes, raisins
Baking staples: arrowroot
starch, baking soda, Extras: coconut wraps,
blackstrap molasses, nori wraps, apple chips,
carob powder, cassava banana chips, cassava
flour, coconut flour, chips, plantain chips,
cream of tartar, gelatin, sweet potato chips (check
honey, maple syrup, palm ingredients for “ no ”
shortening, sweet potato foods), coconut flakes,
flour, tapioca starch coconut milk or cream

Root vegetables and alliums: Fresh fruit: apples,

fresh garlic, ginger root, avocados, bananas
onions, sweet potatoes,
winter squash

Some pantry items require refrigeration after opening. For long-term storage of alliums, roots, and fruit, put them in the fridge.

123 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 WHAT’S
IN THE
FREEZER

• Broth
• Meat: ground beef
• Fish and shellfish: salmon,
tilapia, shrimp
• Vegetables: artichoke
hearts, broccoli, carrots,
cauliflower, celery, onions
• Fruit: bananas, berries,
Frozen prepared mangoes, pineapple
foods: soups, stews, • Fresh herbs: basil, mint,
casseroles, cooked oregano, rosemary,
meat dishes tarragon, thyme (to best
retain the flavor of fresh
herbs, chop and mix with
olive oil before freezing)

Fresh or
thawed meat WHAT’S
and seafood: IN THE
bacon, ground FRIDGE
beef, pork

Open pantry items:

coconut aminos,
fish sauce, olives,
raw vinegars

Cold beverages:
iced herbal tea,
kombucha, mineral
water

Fresh produce:
berries, carrots,
celery, cucumbers,
kale, lemons, lettuce

Avoid freezing salads, delicate herbs, and hot foods that have not been cooled. The best containers for freezing are
freezer-safe glass containers with tight-fitting lids, plastic freezer bags, and plastic lidded containers.

124 THE AUTOIMMUNE PROTOCOL

Subscribe at: PaleoMagazine.com The AIP Guide 65
by Dr. Sarah Ballantyne, PhD
 FOOD QUALITY
In general, it’s best to consume whole and fresh foods,
which means foods made from unprocessed, unmanipulat-
ed ingredients and foods in their most natural state and as
close to harvest as possible. Both processing and storing
foods depletes their nutrients. It’s still okay to stock your
pantry and have a variety of flavoring ingredients in the
door of your fridge, but the vast majority of the foods you
cook with should look as close as possible to how they
look while growing or roaming in the wild. And when
farm-fresh isn’t an option, buying frozen is typically just
as good.

The higher the quality of your foods, the more

nutrients they contain. While eating solely
from the pinnacle of food perfection is not
typically necessary to see great improvements
in health, knowing what the best options are
is still important.

For red meat and poultry, high-quality means grass-fed if the animal is an herbivore (like a cow, buffalo,
or lamb), pasture-raised if the animal is an omnivore (like a pig, turkey, or chicken), or wild if the animal
is a game animal (like deer or boar). For all these animals, high-quality sourcing means leaner and more
vitamin- and mineral-rich meat with healthier fats (most notably, a better ratio of omega-6 to omega-3
fatty acids, but also some other health-promoting fats, like conjugated linoleic acid) that’s never been
treated with antibiotics or hormones.

For seafood, high-quality ideally means wild-caught from the ocean or from unpolluted lakes, rivers,
and streams. However, farmed fish is still a great option (and far better than not eating fish at all); it pro-
vides high levels of beneficial omega-3 fatty acids (DHA and EPA), highly digestible protein, and a pletho-
ra of vitamins and minerals that are essential for thyroid and immune function.

For produce, high-quality ideally means fresh, locally grown, organic, and in-season vegetables, fruits,
and herbs. This may not be practical where you live, but whatever produce you can source from local
farmers or grow in your backyard will be more nutrient-dense than even organic produce purchased
from a grocery store. Frozen organic vegetables and fruits are the next best thing to fresh, since they are
frozen very soon after being harvested and are harvested ripe at the peak of the season. For mushrooms,
wild is best, and for dried herbs and spices, the best choice is organic.

125 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Animal fats like lard or tallow should come from grass-fed
and pasture-raised animals or wild game. Plant fats like
coconut oil and olive oil should be cold-pressed, ideally
completely unrefined, and as fresh as possible.

Eating the best-quality foods that you can source is very

important, but if you can’t afford these high-quality ingre-
dients or you don’t have access to them where you live, it’s
not a nonstarter. Even conventionally grown and raised
food from the grocery store will typically have you feeling
better on the AIP.

126 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SOURCING QUALITY
INGREDIENTS
If you’re intrigued by the extra benefits that comes from the
best-quality foods, you may be wondering where you can find
them.

LOCAL FARMERS
(farmers markets, farmstands, pick-your-own farms, farm shares,
community-supported agriculture, and co-ops):
Sourcing food from local farmers is one of the best ways to
maximize the quality of your food and can be a vital tool for
getting high-quality food on a tight budget. It’s also a great way
to get organ meat, buy a half or whole butchered animal, and
find vegetables and fruits that you might not be familiar with.

SPECIALT Y STORES
(health-food stores, natural-food stores, supplement stores,
cultural food markets, and co-ops):
From big-chain natural-food stores to mom-and-pop cultural food markets, these stores can be a boon
to seekers of unusual ingredients and high-quality foods. Even supplement stores and small health-food
stores often stock local produce. Cultural markets are a great place to find unusual fruits and vegeta-
bles, although they’re typically imported unless there’s a large ethnic community to cater to, in which
case they may be locally grown.

ONLINE
Frozen high-quality meat and seafood, farm-fresh produce, and the full range of pantry ingredients
used in this cookbook are all available online. In fact, these foods are often cheaper online than in stores
(though not always, so make sure to compare prices!). And there’s something about the convenience of
having foods delivered to your door that can’t be beat.

SOME OF THE MOST RELIABLE ONLINE VENDORS ARE:

One Stop Paleo Shop Amazon.com

ºº ShopAIP ºº Farmbox Direct
ºº Thrive Market ºº ButcherBox
ºº Epic Bars, Broth & Animal Fats ºº US Wellness Meats
ºº Tropical Traditions ºº GrassFed Traditions
ºº ºº

127 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 REGUL AR OL’ GROCERY STORES:
Never fear if the above food vendors are beyond your reach,
either geographically or budgetwise. More and more grocery
stores are stocking grass-fed meat, free-range chicken, wild-
caught fish and shellfish, and organic vegetables and fruits. Most
of the pantry ingredients used in this cookbook can be found
pretty easily in most grocery stores, and if your grocery store has
an organic food aisle, gluten-free aisle, or vegan/vegetarian food
aisle (these are often combined into one space), and/or a cultural/
international foods aisle, these can be great places to find some
of the more unusual pantry ingredients. When in doubt, ask
someone at the store—while not all grocery stores are willing to
special-order foods, if a store perceives a market for an
ingredient it doesn’t usually carry, it may hop on the bandwagon.

But don’t worry if your local grocery store doesn’t carry anything more than the industrially produced
basics or if those higher-quality options are simply beyond your budget. You can still see substantial
improvements in your health! Simply chose fresh or frozen plain meats, vegetables, seafood, and fruits—
that’s really all there is to it.

128 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 NAVIGATING YOUR
GROCERY STORE
navigating your grocery store
One of the biggest changes you may see in your shopping Grocery stores are all laid out slightly differently, but in
is how you navigate your grocery store. You’ll likely never general, here’s the path you’ll likely take through your
go down many of the interior aisles that used to be your grocery store and what you’ll find where.
go-to aisles for every trip to the store.

MEAT SEAFOOD
DAIRY

BAKERY
WINE
20

19

18

LAUNDRY, PERSONAL HYGIENE 17

HOUSEHOLD SUPPLIES, DENTAL, TRASH BAGS 16

15

14
13

12

HARDWARE, HOUSEHOLD GOODIES 11

10

PASTA, CRACKERS, COOKIES, VINEGARS 7

INTERNATIONAL FOODS, PICKLES, OLIVES 6

5
4
CHIPS, PRETZELS, POPCORN
FROZEN FOODS

FROZEN FOODS

FROZEN FOODS

KITCHEN
JUICE, MIXERS

CLEANING PRODUCTS,
SOFT DRINKS

BAKING, OILS
COSMETICS

BATH TISSUE, BABY

BREAD, CANDY

NATURE'S MARKET
COFFEE SHOP
CANNED FOODS

CHEESE
OLIVES
DELI

BISTRO
VITAMINS
SEASONAL PROMO FLORAL
PHARMACY

OVER-THE-COUNTER CUSTOMER
SERVICE

CHECKOUT LANES PRODUCE

RESTROOMS

Produce Section Baking Aisle International Foods Frozen Foods Aisles

Fresh vegetables Avocado oil Aisle Frozen broccoli
Fresh herbs Coconut oil Coconut aminos Frozen carrots
Fresh fruit Dried fruit Coconut milk Frozen chicken breast
Dried herbs Fish sauce Frozen salmon
Olive oil Nori wraps Frozen shrimp
Meat Section
Sea salt Olives
Fresh meat
Spices
Bacon Canned Foods Aisle
Unsweetened shredded Nature’s Market Canned fish
coconut
(organic/gluten-free) Canned pumpkin
Seafood Counter
Arrowroot starch Coconut milk
Fresh fish
Tapioca starch
Fresh shellfish
Carob powder
Palm shortening
Plantain chips
Sweet potato chips

58 what and how to eat

129 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CHOOSING ORGANIC
Many pesticides are known to negatively impact the im-
mune system (although there remains an urgent need for
more research on this topic). The effects of these chemi-
cals can be broadly categorized as either suppression or
inappropriate stimulation of the immune system—both
of which can be hazardous to people with chronic illness.
Furthermore, many pesticides affect the composition of
the gut microbiome, skewing toward dysbiosis.

The most immunotoxic class of pesticides is organochlo-

rinated pesticides (many of which are now illegal, and
some are even banned globally). These pesticides increase
inflammation, decrease the ability of the immune system
to regulate itself, suppress critical components of the im-
mune system that are needed to detect and kill cancerous
cells, and can even increase autoantibody production in
people with autoimmune disease. While they are mostly
being phased out of agricultural use, newer pesticides
may contribute to immune-function problems. Studies have linked organophosphates and carbamates
(both widely used as insecticides) to changes in immune cell activities, stimulating some cell types while
suppressing others. The widely used agricultural pesticide tributyltin chloride, an organotin pesticide,
has been shown to cause cell death in the thymus gland. Atrazine, another organotin pesticide, as well
as the insecticide propanil are known to reduce numbers and activities of specific immune cell types.

As scary as this sounds, most of the studies evaluating the effects of pesticides on the immune system
mimic occupational exposure rather than the much lower exposure that the majority of us would have
simply by eating produce from crops treated with these chemicals.

While large epidemiological studies on the correlation between insecticides and chronic
disease have not been performed, the Women’s Health Initiative Observational Study
did show a positive correlation between insecticide use (as in, in your garden) and the
risk of both rheumatoid arthritis and systemic lupus erythematosus.

What effect the very small amounts of these chemicals that might be found on conventional
produce causes either in a healthy person or in someone with chronic disease remains unknown.

130 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
Glyphosate (the active ingredient in Monsanto’s weed kill-
er Roundup) is a broad-spectrum herbicide that can kill both
grasses and leafy weeds. It works by inhibiting an enzyme
(5-enolpyruvylshikimic acid-3-phosphate synthase, or EPSP
synthase) in plants that’s needed to synthesize the amino acids
tyrosine, tryptophan, and phenylalanine (which are essential
for plant growth). The pathway this affects (the shikimic path-
way) doesn’t exist in animals, which is part of why glyphosate
is considered to have low toxicity in animals. In the US, glypho-
sate has been used for over 40 years and is used mostly to kill
weeds that interfere with agricultural crops (typically corn,
soy, and canola). However, new evidence shows that glypho-
sate has been shown to disrupt gut microbiome composition,
increasing the ratio of pathogenic bacteria to helpful microbes,
promoting a reduction of Bifidobacteria, Lactobacillus, and
Enterococcus while supporting an increase in Salmonella and Clostridium (which are resistant to glypho-
sate). Chillingly, this occurs even at levels well below the US Acceptable Daily Intake (ADI). In fact, there
is no strong dose response: very similar microbiome changes are seen at glyphosate exposures as low 0.1
ppb and as high as 5000 ppm (note the parts per billion [ppb] versus parts per million [ppm]). And, just for
relevance, results from third party testing of 85 tap water samples by Moms Across America and Sus-
tainable Pulse, 35 of the samples had glyphosate levels up to 0.3 ppb. And glyphosate contamination in
non-organic food is very common, with levels up to even 500 ppb in something like wholewheat bread.
This is an excellent additional reason to avoid grains, but also to filter tapwater by reverse osmosis.

While the benefits of eating a vegetable-rich diet almost certainly outweigh the health detriments from
pesticides for those consuming exclusively conventionally grown produce, reducing pesticide exposure
is very sensible. The easiest way to do so is to buy organically grown
produce whenever possible. Certain food crops tend to have more residu-
al pesticides than others, so familiarizing yourself with the “Dirty Dozen”
is a good way to prioritize which foods to buy organic if budget is a con-
cern. The Dirty Dozen is a list compiled every year by the Environmental
Working Group of the foods that contain the highest amounts (and the
most different types) of pesticides. (The EWG—www.ewg.org—also puts
together a Clean Fifteen list of the fifteen crops with the least amount
of pesticides.) As a general rule, apples, stone fruits, berries, and leafy
greens are veterans of the Dirty Dozen list. Another way to lower your
pesticide exposure is to peel fruits and vegetables before eating them.
(For example, peeling apples removes the majority of the pesticides.)
 Quality Water in Your Home
An AquaTru is a compact countertop reverse osmosis water filter, making it the most affordable
way to ensure glyphsate is removed from your tapwater before consumption (note that
glyphosate is not removed by carbon filters). Learn more here.

Once filtered, adding mineral drops to

water can be a great and easy way to up
your calcium, magnesium, and potassium
intake as well as other important electro-
lytes and trace minerals. The combination
of two different brands of electrolyte
drops—CencenTrace Trace Mineral Drops
and Watermins EM Drops—is an excellent
wayto up the mineral content of your
water. Both are unflavored and provide
different minerals (there’s a little overlap,
for example they both contain potassium,
but Concentrace is much higher in
magnesium and trace minerals whereas
EM drops has more calcium).

132 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GUIDE TO EATING
54 1. The Rationale: The Science Behind the Framework

SEASONALLY GUIDE TO EATING SEASONALLY

Eating seasonally simply means choosing only those fruits and best-quality produce) is to do the bulk of your shopping
vegetables that are in season, typically grown locally. Of course, at local farms and farmers markets. This may or may not be
this will vary depending on the climate you live in. For example, practical depending on where you live, so you may need (or
strawberries and asparagus are usually harvested beginning want) to supplement with produce from the grocery store (in
in late spring, peaches and cherries in summer, apples in fall, season, even if not grown nearby). Fruits and vegetables also
and citrus fruits and cruciferous veggies like kale and Brussels tend to be cheaper when they are in season (since supply is
sprouts in winter. An easy way to eat seasonally (and eat the high), which is great for anyone on a tight budget.

apricots limes spring onions apricots blueberries loganberries

artichokes mangoes strawberries arugula boysenberries melons

arugula mustard greens Swiss chard Asian pears broccoli nectarines

asparagus oranges turnips beets cherries okra

beets pineapple Vidalia onions black currants cucumber passion fruit

broccoli radicchio watercress blackberries figs peaches

cauliflower rhubarb wild leeks (aka garlic pineapples

ramps)
chives sorrel grapes plums

collard greens spinach kiwi radishes

fennel spring greens limes raspberries

(baby lettuce) SUMMER
fiddleheads strawberries

garlic summer squash

grapefruit Swiss chard

honeydew zucchini

jicama SPRING
kale

kohlrabi

WHAT’S IN SEASON WHEN*?

apples
Jerusalem
bok choy artichokes

Brussels sprouts
WI N T E R FA L L
jicama

cauliflower kale

cherimoya kohlrabi

clementines kumquats

coconuts cauliflower passion fruit

collard greens cherimoya pears

dates passion fruit coconuts pomegranate

grapefruits pears cranberries pumpkin

jicama persimmons apples daikon radish quince

kale pineapple arugula garlic radicchio

kiwi pomegranate sweet potatoes Asian pears ginger rutabagas

kohlrabi pomelo tangerines bok choy grapes sweet potatoes

limes red currants winter squash broccoli guava Swiss chard

oranges rutabagas yams Brussels sprouts huckleberries winter squash

Y EA R- R O U N D
avocados broccolini celery lemons onions shallots

bananas cabbage celery root lettuce papayas turnips

beet greens carrots leeks mushrooms parsnips

133 THE*Based
AUTOIMMUNE
on North AmericanPROTOCOL
harvests. Varies regionally.
by Dr. Sarah Ballantyne, PhD
EXTRA VIRGIN
OLIVE OIL
The Healthiest Fat
Olive oil is consistently linked with health benefits,
including reducing cardiovascular disease risk (including both
heart disease and stroke), reducing Alzheimer’s disease risk
(more research is needed), reducing cancer risk (more studies
are needed), improving blood sugar regulation and insulin
sensitivity, reducing likelihood of weight gain (and maybe
even aid in weight loss), reduce reducing joint pain and swelling
in rheumatoid arthritis, and generally reduce markers of
inflammation (like C-reactive protein). These benefits are attributable to its high content of the
monounsaturated omega-9 fatty acid, oleic acid, making up 55 to 83% of olive oil, and the fact that
high-quality olive oil is very rich in at least 30 phenolic compounds with antioxidant activity—
particularly oleuropein, hydroxytyrosol, tyrosol—as well as alpha-tocopherol, an important form
of vitamin E.

Many of the health benefits associated with olive oil are related to its effects on the gut microbiome.
A recent mouse study tested the effects of several three-month-long diets with different fat com-
positions: one with 38% of calories from extra virgin olive oil, one with 38% of calories from refined
olive oil, one with 38% of calories from butter, and one with a standard low-fat chow. At the end of the
study period, the extra virgin olive oil resulted in the most favorable microbial profile (significantly
different than that of butter, which resembled the microbiota composition seen in obese individuals).
The refined olive oil resulted in intermediate changes to the microbiota (different than butter, but less
dramatically so than extra virgin olive oil), suggesting that olive oil is beneficial not only due to its fat
composition, but also due to the polyphenols present in extra virgin varieties. This has been confirmed
in several additional studies, showing that extra virgin olive oil leads to a more diverse gut microbi-
ome, supporting the growth of probiotic bacteria that are linked to improved insulin and leptin
regulation as well as a healthier metabolism.

Another important reason to choose a extra virgin when it comes to olive oil is heat stability. A
number of studies have been conducted on olive oil to assess the effects of cooking on its structure and
nutritional content, as well as what happens in the human body after olive oil is ingested. Across the
board, the research shows that even with a fair amount of heat exposure, extra virgin olive oil resists
oxidation better than many other cooking oils. In one study, it took over 24 hours of frying before the
olive oil generated enough polar compounds to be considered harmful. In another study, even after 36
 hours of cooking, the olive oil had retained most of its beneficial vitamin E content. In fact, high-
quality (low-acid) extra-virgin olive oil can have a smoke point as high as 410°F, which is higher than
most cooking applications and makes olive oil (at least the good stuff) more heat-stable than many of
our other go-to cooking fats.

Choosing the Best Olive Oil

How do we choose the best olive oil? A few simple tips can help:

ºº tell you when the olives were picked. The more recent the date,
Look for brands that list a harvest date on the bottle, which will

the better (no more than 12 to 18 months)!

ºº
Always choose oils in dark glass bottles—never plastic or clear ones.

ºº (and even cut with non-olive vegetable oils—yikes!), so look for more local oils,
Oils imported from other countries are more likely to be deceptively labeled

especially ones from California, or choose oils from domestic companies that
are transparent about their Mediterranean sources and production practices.

ºº a bit—that’s a sign of a high polyphenol content.

The oil should taste pungent and peppery, even stinging the back of your throat

ºº
Make sure that the label says “extra-virgin” and not “refined.”

ºº
Fresher is better. Unlike vinegar or wine, olive oil does not get better with age.

ºº
Store in a cool, dark place and use within 6 months!

135 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MEAL IDEAS
BREAKFAST . Think of breakfast as including a protein,
like meat, and some veggies and/or fruit. Your protein could
come from bacon, sausage, or even steak or a pork chop.
Leftover meat from last night’s dinner makes for a very quick
breakfast. Your sides could include any fresh fruit. Vegetables
can be raw (like mixed greens, or carrots and celery sticks),
sautéed (a great pairing for bacon) or steamed, fermented
(homemade or raw sauerkraut makes a great accompaniment to
sausage) or leftovers of any kind. Many root vegetables make
for delicious breakfast hash. Soup also makes for a satisfying breakfast. Smoothies can be made with
veggies, fruit, coconut milk, and AIP-friendly protein powder like collagen peptides.

LUNCH . Just like breakfast, think of lunch as including some animal foods and some plant foods.
Lunch can look very much like supper with some kind of protein and some kind of vegetable side dish
or dishes. Or lunch could be a salad that includes some leftover chicken or steak or pre-cooked shrimp.
Soups and stews make for a quick lunch as do reheated leftovers. If you’re really used to sandwiches, you
could make them with lettuce or nori wraps instead. Looking for something really easy to eat on the go?
Try jerky with some raw veggies and guacamole and some fruit or sweet potato chips.

DINNER . Dinner may be the easiest meal for people to adapt to the AIP diet, simply because the old
standby of meat-and-potatoes is already halfway there. Instead of potatoes, you can include any starchy
vegetable. Any number of vegetables and even fruit can easily find its way on the side of meat, poultry
or fish. Many soups and stews can be easily adapted with some simple ingredient substitutions.

SNACKS . Apples or celery with coconut or tigernut butter, plantain chips with uncured deli meats,
or canned fish, fruit, and AIP-friendly jerky or Epic bars make quick, delicious snacks. Handy Pre-pack-
aged On The Go Foods. Jerky, Epic bars, Sea Snax, plantain crackers, sweet potato chips, and fruit and
vegetable leathers are all great AIP-friendly convenience foods.

136 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Ready-Made Meals
Paleo on the Go offers pre-made Paleo meals delivered right to your door. I partnered with
them to create a menu that is 100% autoimmune-friendly!

Handy Prepackaged On-the-Go Foods**

ºº
New Primal Jerky*

ºº
Epic bars, bites, and snack strips*

ºº
Chomps Snack Sticks*

ºº
Seaweed snacks*

ºº
Plantain chips (Artisan Tropic, Inca)

ºº
Sweet potato chips (Honest Jackson)

ºº
Cassava chips (Artisan Tropic)

ºº
Fruit and vegetable leathers (Veggie Gos)

ºº
Pork Rinds (Epic, Pork Clouds)*

ºº
Paleo Angel PowerBalls*

ºº
Sweet Apricity Caramels and Marshmallows*

ºº
Vital Proteins Collagen Veggie Blend

ºº
Vital Proteins Beef Liver

ºº
Sweetpotato Awesome*

ºº
That’s It Bars

ºº
Wild Zora meat & veggie bars*

* always check ingredients, not every flavor is AIP

** It’s nearly impossible to list all the amazing and convenient AIP products these days! You can find new
products that have already been verified as 100% AIP either on ShopAIP.com or OneStopPaleoShop.com’s
AIP section.

137 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Handy Pantry Items to Have on Hand**
ºº Cassava flour (Otto’s)
ºº Tapioca starch
ºº Arrowroot starch
ºº Coconut flour
ºº Extra virgin olive oil
ºº Extra virgin coconut oil
ºº Palm shortening
ºº Coconut aminos
ºº Fish sauce*
ºº Epic animal oils
ºº Avocado oil
ºº Bone broth (Epic, Bare Bones)*
ºº Beet Lady ketchup and marinara
ºº KC Naturals seasonings, sauces, condiments, and salad dressings
ºº Paleo Powder AIP All-Purpose Seasoning
ºº Primal Palate Everyday AIP Seasoning blends
* always check ingredients, not every flavor is AIP
** It’s nearly impossible to list all the amazing and convenient AIP products these days! You can find
new products that have already been verified as 100% AIP either on ShopAIP.com or OneStopPaleo-
Shop.com’s AIP section.

138 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Y- S AV I
NE N
O
C HE A PE ST O PTIONS

G
BEEF PORK CHICKEN SEAFOOD
chuck roast Boston butt whole chicken canned
ground beef ground pork chicken thighs pouched
ST
R AT E G I E S
sirloin belly ground chicken frozen
tri-tip loin liver cod
liver heart tilapia
4 Know the average prices for foods heart
and shop around (including online) kidney
4 Clip coupons bones
4 Shop sales VEGETABLES FRUITS
4 Buy in bulk
4 Haggle or barter FROZEN
4 Grow your own FOODS
apples
cabbage lettuce
“ LONGCUTS ” TO SAVE MONEY
(NOT SHORTCUTS, BUT WORTH THE EFFORT)
4 Buy bigger cuts of meat, which are typically carrots onions avocados veggies
cheaper per pound, and butcher them yourself
or roast whole and freeze leftovers
bananas
4 Buy tough cuts of meat that take longer to cook
4 Buy veggies in bulk rather than washed and spinach fruits
chopped in packages
celery berries
4 Buy meat, seafood, veggies, and fruits when
heavily discounted and freeze them yourself sweet potatos
seafood
cucumbers
SURPRISING WAYS HEALTHY FOOD AND
olives
L IFESTYL E CHOICES WILL SAVE YOU MONEY
4 You’ll no longer eat at fast food joints or
restaurants or grab prepared foods kale plantains meats
winter squash
4 You’ll cut out completely or cut down on (frozen is usually much
expensive beverages like soda, fancy coffee cheaper than fresh)
drinks, beer, wine, and spirits FOODS THAT GIVE YOU A
GOOD BANG FOR YOUR
4 Walking or cycling more will save you money on gas
BUCK (AND YOUR HEALTH)
4 You may reduce the need for medications,
supplements, and doctor visits canned seafood
(wild salmon,
mussels, oysters,
CHEAP VEGGIES THAT STRETCH A MEAL high-quality
olives olive or coconut oil
avocados

chicken livers frozen organic leafy greens

and any other frozen (kale, Swiss
berries spinach
organ meat) chard, spinach,
butternut cabbage collard kale dandelion greens)
squash greens

cruciferous sweet
veggies (arugula, potatoes
Brussels sprouts, mushrooms
plantains rutabagas sweet turnips cabbage, kale)
potato winter sea salt
squash
70 AUTOIMMUNE
THE The AIP Guide PROTOCOL
139
by Dr. Sarah Ballantyne, PhD
 TIPS FOR EATING IN
RESTAURANTS AND TRAVEL
It can be tricky to stick with the AIP when you eat out, but it is possible. It helps to know exactly which
foods you fully tolerate, which ones you can tolerate in small, occasional amounts, and which are
totally verboten for you, knowledge that you can only glean through methodical reintroductions.

If you are going out to eat, it’s a good idea to call ahead and make
sure that the restaurant can accommodate you.
For most people, remaining gluten-free is the top priority, but you’ll also want to avoid any other
foods that elicit a reaction when you eat them, like soy, dairy, or tomatoes. Knowing what line you
personally cannot cross is key to navigating restaurants. Fortunately, many restaurants are develop-
ing gluten-free menus and have gluten-free workspaces to cater to those with celiac disease or gluten
sensitivities. There are also a growing number of Paleo-friendly restaurants, most of which can easily
accommodate additional dietary restrictions like the AIP. Farm-to-table restaurants are usually a good
bet, as are burger chains that specialize in grass-fed beef.

It is important to have an open dialogue with your server. Explain which foods you cannot eat. (Even if
they’re not technically allergies, it can sometimes be helpful to express them as such to get the staff
to take your needs seriously.) Ask specific questions: Is that meat dredged in flour before cooking? Is
there any dairy in that salad dressing? What seasonings are used? Find out which dishes can be made
to order: Can the fish be grilled instead of fried? Can you get a hamburger without the bun? And ask if
the chef is amenable to making something off the menu for you. (That’s a good question to ask before
you arrive.)

140 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Certain foods are more likely to be “safe” than others. Generally, grilled or roasted meats, grilled
or poached seafood, salads (ask for the dressing on the side), and grilled or steamed vegetables
can be ordered with a much greater certainty of being AIP-friendly. They might not be cooked in
the best-quality fats, but most people will tolerate these on occasion.

When it comes to eating at someone else’s house, you should talk to your host beforehand. Ex-
plain what you can’t eat—and also what you can! Make sure your host understands which foods
might be hidden sources of gluten, like bottled sauces. It can also help to offer to bring some-
thing you can eat: maybe a protein if you know that item will be the hardest for your host to
prepare, or a side dish or dessert to share.

Traveling can be a challenge as well. For a road trip, it’s best to haul out and stock the cooler
so you know you’ll have good eats along the way. If you have to hit the grocery store to top off
your supplies during a longer trip, look for rotisserie chickens (check the ingredients!), deli meats
(again, check the ingredients!), canned fish or tuna in pouches, sweet potato chips, plantain chips,
and raw vegetables and fruit. There are also slow cookers and microwaves that can plug into
your car to reheat food.

Many of the same “convenience” foods work for air travel. If you are traveling internationally,
check the regulations ahead of time to find out which food items you can bring with you. Gen-
erally, nonperishables such as jerky, meat-based protein bars, dried fruit, packaged plantain or
sweet potato chips, and canned fish are okay. Depending on whether you technically cross an
international border before your flight or afterward, you might be able to bring perishable food
on the plane but then be required to toss any leftovers before going through customs.

Eat a balanced meal before you leave home and have a plan for how to source good food once you
arrive at your destination. If you’re staying at someone’s house, talk to your host ahead of time;
if you’re staying at a hotel, scope out the closest grocery store or specialty stores before you
arrive. Spending a little extra for a hotel room with a mini-fridge or, better yet, a kitchenette
will make your life much more pleasant. Then all you have to do is bring a paring knife or pocket
knife (in your checked baggage!), a few utensils (camping utensils are very versatile), and maybe
even a jar or two of your favorite fat or oil, seasoning mix, or good-quality salt, and you will have
it made in the shade in terms of sticking with AIP far from home.

The bottom line is that the best way to eat well away from home is similar to eating well at
home: plan ahead! And do a little troubleshooting before you get in trouble: What will you do if
your plane is delayed? If you arrive at your friend’s house and discover that he marinated the
pork in barbecue sauce that contains gluten? If the grocery store is closed by the time you get
to your hotel? In some cases, not eating will be a better choice than eating a food that you know
will cause an increase in symptoms. In other cases, eating a suboptimal food will be a better
choice than enduring the stress of not eating. And you can avoid both of those contingencies by
packing some emergency food.

141 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 LEARN MORE

The Paleo Mom Workshop & Masterclass 2019

Dr. Sarah Ballantyne hosted a 3-day workshop and retreat during the long weekend of February 15-18, 2019
at an inspiring and unique learning center in the redwoods of Santa Cruz County, California—1440 Multiversity!
Couldn’t make it in person? Feel like you were in the room with instant digital access to ~15 hours of
high-quality video recordings and printable PDFs of the 600+ slides for every program session, plus photos,
testimonials, and anecdotes from this extraordinary and profound event

Recharge your health journey with the latest science-grounded information on a variety of diet and lifestyle
topics relevant to you! The program session curriculum included the following topics:

ºº
An Introduction to Nutritional Sciences

ºº
The Foundations of Health

ºº
The Modern Scientific Tenets of Optimal Human Diet and Lifestyle

ºº
Best Practices to Prevent and Mitigate Chronic Disease

ºº
An Introduction to the Autoimmune Protocol

ºº
Gut Health as the Key to Lifelong Health

ºº
Best Practices for Gut Barrier and Microbiome Health

ºº
Shifting Focus: Getting Healthy to Lose Weight

ºº
Best Practices for Healthy and Sustainable Weight Loss

ºº
The Problem with the Low-Carb Craze and Other Fads

ºº
Functional Approaches to Troubleshooting Health Challenges

Sign up for the live workshop in 2020 SIGN UP!

142
 PA R T F O U R

Reintroductions, Gray
Areas and Troubleshooting
143 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 REINTRODUCING FOODS
The autoimmune protocol can be thought of as a nutritional intervention for a diet gone badly awry,
overabundant in calories and lacking in vital nutrients. But how well an individual tolerates subopti-
mal foods—whether we’re talking about something like tomatoes, which are included in the Paleo diet
but eliminated on the autoimmune protocol, or something like grains, which are not included in either
nutritional approach— depends on nutrient status, stress, sleep, activity level, genetics, and health his-
tory. As we improve these factors with diet and lifestyle changes, it’s fairly common to see tolerance
of certain foods increase.

The autoimmune protocol is an elimination diet at its core (following AIP guidelines
100% is often termed the elimination phase), designed to cut out the most likely food
culprits while flooding the body with nutrients. And the best part about an elimination
diet is that, eventually, you get to reintroduce foods that you’ve been avoiding.

How long is eventually? Ideally, you’d wait to reintroduce foods until you feel amazing, but as long as
you’re seeing improvements in your health thanks to your diet and lifestyle changes, you can try some
reintroductions even as early as after three to four weeks. It’s best not to be in a hurry to reintroduce
foods. Generally, the longer you wait, the more likely you are to be successful.

Ultimately, when you introduce particular foods is your choice. How you feel is the best gauge, and
only you will know if you are ready. A word of caution, though: don’t let cravings influence you.
Your decision should be based on how good you feel and how much improvement you’re seeing in
your disease.

In general, reintroduce only one food every five to seven days,

and spend that time monitoring yourself for symptoms of a
reaction. Ideally, you should avoid food reintroductions until
your disease is in full remission. Your decision should come
from feeling good and seeing improvement, not cravings. If
you think your immune system is still attacking your organs,
then it is too early for reintroduction.

It’s best not to be in a hurry to reintroduce foods. Generally,

the longer you wait, the more likely you are to be success-
ful. Ultimately, when you introduce particular foods is your
choice. How you feel is the best gauge, and only you will know
if you are ready. A word of caution, though: don’t let cravings
influence you. Your decision should be based on how good you
feel and how much improvement you’re seeing in your
THE AUTOIMMUNE PROTOCOL disease.
144 by Dr. Sarah Ballantyne, PhD
 Don’t reintroduce a new food if you have an infection, have just had an unusually strenuous workout,
got less sleep than normal, are feeling unusually stressed, or are under any other circumstances that
may make interpreting a reaction difficult. If you have a hard time determining which food caused
what reaction, wait longer between reintroductions. Even if a reintroduction is successful, you may
wish to keep your consumption of the food to a minimum (like reserving a glass of wine for Sunday
dinner) for the best long-term results. The foods you tolerate may change over time, so a failed
reintroduction does not mean you can never eat that food again.

Some foods that you reintroduce will also be relegated to “sometimes foods.” These will include
alcohol and potentially some of the stage 4 reintroductions (see “Suggested Order of Reintroductions”
on next page), like gluten-free grains. A sometimes food is one that doesn’t cause a reaction when you
consume it occasionally, but that can subtly undermine your health (even if simply by displacing more
nutrient-dense options) if you consume it on a regular basis. These are still worth reintroducing, even
if they aren’t going to make it into your normal rotation, because they give you more flexibility in situ-
ations like travel and eating out.

145 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 HOW TO REINTRODUCE FOODS
symptoms of aOF
SYMPTOMS reaction aren’t
A REACTION always
AREN’T obvious
ALWAYS so keep
OBVIOUS,
an eye
SO KEEP outOUT
AN EYE for FOR
any ANY
of the following:
OF THE FOLLOWING:

 Increased mucus  Coughing or increased  Headaches

production: phlegm, need to clear your (mild to migraine)
runny nose, or throat
 Dizziness or
postnasal drip
lightheadedness
 Itchy eyes or mouth  Sneezing
 Feeling anxious, less

able to handle stress

 Mood issues: mood swings,

 Reduced energy, fatigue, or energy
feeling low or depressed
dips in the afternoon, or a second
wind in the late evening that makes
it hard to go to sleep at a good time

 Aches and pains:

 Trouble falling asleep or staying asleep, or
muscle, joint,
just not feeling well rested in the morning
tendon, or ligament

 Gastrointestinal symptoms:  Cravings for sugar, fat,  Changes in skin: rashes, acne,

tummy ache, heartburn, salt, or caffeine dry skin, little pink bumps or

nausea, constipation, diarrhea, spots, dry hair or nails

change in frequency of bowel  Pica (craving

movements, gas, bloating, minerals from nonfood
undigested or partly digested items like clay, chalk,  Symptoms of any diagnosed
food particles in stool dirt, or sand) disease returning or worsening

THE STANDARD PROCEDURE FOR FOOD CHALLENGE IS AS FOLLOWS:

ait 15 m ait 1 5 m
W W
in

in
utes

utes

1. Select a food to challenge. 2. The first time you eat the 3. If you experience any 4. If you experience any
Be prepared to eat it two food, eat 1/2 teaspoon symptoms, don’t eat any symptoms, don’t eat any
or three times in a day, or even less (one teensy more. If you don’t, eat more. If you don’t, eat 1
then avoid it completely little nibble). Wait 15 1 teaspoon of the food 1/2 teaspoons of the food
for a few days. minutes. (a small bite). Wait 15 (a slightly bigger bite).
minutes.

2 to
a it
W
3

5 to 7
ho u

days
rs

5. That’s it for now. Wait 2 6. If you still haven’t 7. Do not eat that food 8. If you have no symptoms
to 3 hours and monitor experienced any again for 5 to 7 days, during the challenge day
yourself for symptoms. symptoms, eat a normal- and don’t reintroduce any or at any time in the
sized portion of the food, other foods during that next 5 to 7 days, you may
either by itself or as part time. Monitor yourself for reincorporate this food
of a meal. symptoms. into your diet.

146 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SUGGESTED ORDER OF
REINTRODUCTIONS
When it comes to food reintroductions, there is no right or wrong way to choose where to start.

A very good argument can be made that the first foods you reintroduce should be the
ones you miss the most. Another argument can be made for reintroducing first the foods
that are least likely to cause a reaction or that have the most redeeming qualities.

The following suggested order of food reintroductions takes into consideration both the likelihood of
reaction (based on what science says about how that particular food interacts with the gut barrier or
the immune system) and the inherent nutritional value of the food. There are four stages. The first stage
includes foods that are most likely to be well tolerated or are the most nutrient dense. The second stage
includes foods that are less likely to be well tolerated or are less nutrient dense. The third stage
includes foods that are even more unlikely to be well tolerated, but still have compelling nutrition.
The fourth stage includes foods that are most likely to be untolerated and that you may wish to never
challenge.

Challenge all the foods in stage 1 that you want to reincorporate (except any that you are allergic to or
have a history of severe reactions to) before moving to stage 2. Follow the same protocol before moving
from stage 2 to stage 3 and then from stage 3 to stage 4. You don’t have to tolerate all the foods in stage
1 to be able to move to stage 2, but if you don’t tolerate many (or most) of the foods, take a break from
new food reintroductions for a few weeks or even months and then rechallenge those stage 1 foods. If
you still react to them, wait a few more weeks and then start challenging stage 2 foods (keeping the
untolerated ones from stage 1 out of your diet).

147 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 S TA G E 1 S TA G E 2
FOODS
1 FOODS 2
egg yolks seeds
ºº fruit-, berry- and seed-based spices ºº nuts
ºº seed and nut oils ºº chia seeds
ºº ghee (from grass-fed dairy) ºº coffee on a daily basis
ºº occasional coffee ºº egg whites
ºº cocoa or chocolate ºº grass-fed butter
ºº peas and legumes with edible pods ºº alcohol in small quantities
ºº (green beans, scarlet runner beans, ºº
sugar snap peas, snow peas, etc)

legume sprouts
ºº

S TA G E 3 S TA G E 4
FOODS 3 FOODS 4
eggplant chili peppers and nightshade spices
ºº sweet peppers ºº tomatoes
ºº paprika ºº unpeeled potatoes
ºº peeled potatoes ºº alcohol in larger quantities
ºº grass-fed dairy ºº gluten-free grains and pseudograins
ºº lentils, split peas, and garbanzo ºº traditionally prepared or
ºº beans (aka chickpeas) ºº fermented legumes
white rice
ºº foods you are allergic or have
ºº a history of strong reactions to

148 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Don’t Be Afraid
It’s a surprisingly common experience to feel so good on
the AIP that a person is afraid to try any reintroductions.
But reintroducing eliminated foods is a critical step of your
health journey. This is because some eliminated foods (like
eggs, nuts, seeds, cocoa, and grass-fed dairy) have some
impressive nutritive value and can improve the overall
nutrient density of your diet if well tolerated. Plus, the more dietary flexibility you have,
the easier life is—you’ll have less difficulty traveling or eating in restaurants or at potlucks,
work meetings, or any social situation.

The knowledge you glean from reintroductions is empowering. If a reintroduction goes well,
you’ve got a new food to add to your diet, increasing the variety of foods you eat. If a rein-
troduction doesn’t go well, this is still great information! You now better understand the
dietary triggers of your disease and which lines you can’t cross. And in the uncommon case
where a reintroduction goes very poorly (the fear of which is what stops many people from
even trying), remember that the AIP is an entire toolkit for healing. You have the knowledge
and skills to recover quickly and get back on your feet. Just go back to 100% AIP, get plenty
of sleep and low-strain activity, and stay hydrated until you feel better.

149 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 STAGE 1 & 2
REINTRODUCTIONS
(aka Gray Area Foods)
The focus of Stage 1 and 2 Reintroductions is foods that have the capacity to greatly benefit our
health, but which might not work for many people with autoimmune disease. These foods are wor-
thy of a little extra discussion because, depending on your individual circumstances, you may opt
not to eliminate one or more of these foods initially (ideally a choice made in conjunction with your
doctor and/or an AIP Certified Coach). These foods earn Gray Area status because responses to them
are individualized, perhaps driven by genetics, and if you are not sensitive, these are foods that can
greatly benefit your health.

Peas, Legumes with Edible Pods & Legume Sprouts

Legumes are members of the pea family (Fabaceae) that produce long seedpods and include
chickpeas, fava beans, lentils, mung beans, soybeans, peanuts, lima beans, alfalfa, great northern
beans, broad beans, cannellini beans, black beans, common beans, kidney beans, red beans, snow
peas, sugar snap peas, wax beans, and green beans… just to name a few!

Legumes are avoided on the AIP due to their high lectin, saponin, and phytate content (including
some lectins that are incredibly toxic). However, the playing field changes when it comes to
edible-podded legumes like green beans (also called string beans or snap beans) and fresh peas
(including sugar snap peas and snow peas). Unlike other legumes, which are harvested after their
seeds (called pulses) have matured and dried, we eat green beans and fresh peas when they’re still
soft and immature.

One result of this involves phytic acid or phytate, the main storage form of phosphorus in plants.
Phytic acid binds to minerals and reduces their bioavailability to us (hence why it’s often called an
anti-nutrient), and tends to be very high in grains, nuts, and legumes.

But, studies of different legume varieties show that phytate levels increase as legumes
get older and harder, so edible-podded legumes are naturally going to be lower in
phytates due to their earlier stage of maturity.
And, the data we have on actual phytate levels in legumes confirms that green beans and fresh peas
are at the very bottom end of the spectrum. For example, one study found that 15 Polish pea variet-
ies had phytate levels ranging from 0.006 to 0.013 grams per 100g of dry weight, which is between
80 and 370 times less than the phytate content of soybeans!

150 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GRAMS OF PHY TIC ACID PER 100G OF LEGUME (DRY WEIGHT)
Kidney beans: 0.61-2.38
ºº
Broad beans: 0.51-1.77
ºº
Cowpeas: 0.37-2.9
ºº
Garbanzo beans: 0.28-1.6
ºº
Lentils: 0.27-1.51
ºº
Soybeans: 1.0-2.22
ºº
Green beans (raw): 0.15
ºº
Green beans (cooked): 0.05
ºº
Polish pea varieties: 0.006-0.013
ºº

Hemagglutinins and Trypsin Inhibitors

in Legumes before and after cooking

Agglutinins Trypsin Inhibitors

(extract minimum dilution causing
agglutination of human erythrocytes) (Trypsin inhibitor units per milligram)

LEGUME RAW CONVENTIONAL RAW CONVENTIONAL

COOKING COOKING

Black bean 12 3 31.0 2.6

Green pea 0 0 2.5 1.6

Mature pea 3 2 3.5 2.5

Lentil 2 0 3.6 2.4

Faba bean 0 0 7.2 3.1

Chickpea 3 2 17.9 3.1

151 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 On top of that, when we eat green beans or fresh peas, we’re not just eating the plant’s seeds like we do
with other legumes: we’re also consuming the pod itself, which doesn’t contain the same kinds of lectins
(or same high level of phytates) that legume seeds do. In fact, the nutritional profile of green beans and
fresh peas is much more similar to non-starchy vegetables than it is to other legumes (including a low
calorie density and high content of vitamin C and vitamin A precursors). For example, if we compare ed-
ible-podded peas (which include both the pod and the peas inside!) with mature split peas (which include
only the seeds inside the pod), we can see that edible-podded peas have a higher concentration of
micronutrients than mature peas. Per 120 calories of food (raw snap peas and snow peas versus cooked
split peas):

%DV of Vitamin and Minerals per 120-Calorie Serving

Vitamin/Mineral Edible-Podded Peas Split Peas

Vitamin A (as precursors) 62% 0%

Vitamin C 296% 1%

Vitamin K 14% 3%

Vitamin B6 23% 2%

Vitamin B9 29% 16%

Vitamin B5 20% 6%

Calcium 11% 1%

Iron 32% 7%

Magnesium 17% 9%

Manganese 35% 20%

152 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 A similar argument can be made for legume sprouts, such
as mung bean sprouts and alfalfa sprouts (noting that al-
falfa sprouts are a common source of fungal contamina-
tion containing mycoestrogens), as the sprouting process
reduces antinutrients while
increasing digestibility and nutrient density.

Furthermore, peas are a microbiome

superfood. Pea protein has been shown
to increase levels of important
short-chain fatty acids in the intestine.
In a rat study comparing the effects of different
legumes in diets with equal protein and calorie levels,
pea consumption resulted in higher counts of Bifidobac-
terium than any other legume tested (including green
beans, chickpeas, and lentils). And, due to its high content
of lysine, pea protein is susceptible to undergoing spontaneous glycation (non-enzymatic bonding of
a sugar molecule to a protein or lipid molecule) during cooking, storage, or after entering the human
body. Researchers investigated the effects of glycated pea protein on human intestinal flora and found
the pea proteins were able to significantly increase levels of Lactobacillus and Bifidobacterium species.
In another study, glycated pea protein was shown to stimulate the adhesion of bacteria to intestinal
epithelial cells, including the adhesion of beneficial lactic acid bacteria, leading to changes in the mi-
crobial composition that would likely benefit the host. In this study, the growth of bacteria from the
genera Lactobacillus and Enterococcus was promoted strongly enough for these bacteria to out-com-
pete members of Escherichia.

Pea fiber is also beneficial. One key study compared the impact on the microbiome of cooked and raw
pea fiber (from the seed coat, eaten when consuming fresh peas) compared to cellulose as a fiber con-
trol in rats with glucose intolerance caused by a high-fat diet. Along with improving glucose tolerance
(cooked pea seed coats only) and reducing insulin response (both cooked and raw pea seed coats), the
peas led to significant shifts in the microbiota composition, including a desirable increase in the abun-
dance of Lachnospiraceae and Prevotellaceae and a decrease in Porphyromonadaceae. These changes
coincided with markers of a healthier gut barrier and increased short-chain fatty acid production.

Of all the early reintroduction foods, peas and legumes with edible pods are probably the most com-
pelling thanks to their very low levels of problematic compounds (likely below threshold for negative
effects for most people with autoimmune disease) and their benefits to the
microbiome and nutrient density.

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 Coffee
A number of research studies show that drinking
coffee in moderation could legitimately provide a range
of health benefits, including reducing the risk of certain
cancers, stroke, diabetes, Parkinson’s disease, Alzhei-
mer’s disease, cardiovascular disease, gout, gallstones,
and depression, along with protecting against antibiot-
ic-resistant bacterial infections and cirrhosis of the liver.
Some of these effects are owed to the antioxidants, poly-
phenols, and bioactive compounds found in coffee, which
can improve insulin sensitivity, reduce inflammation, and
improve the composition of the gut microbiome. Some of
the health benefits of coffee are also directly attributable
to its caffeine content (which is why drinking tea—which
is rich in antioxidants and polyphenols while also containing caffeine—is also associated with
good health). This is partly why many of the health-protective effects of coffee are not seen with
decaf coffee. In addition, the decaffeination process tends to strip the coffee not only of much
of its caffeine content, but also of many of its antioxidants and polyphenols (potentially leaving
behind a few of the more harmful substances that can be found in coffee).

Unfortunately, coffee interacts with the immune system in a way that is both
complicated and highly individualized, which is why coffee is best eliminated
initially on the AIP.

Generally-speaking, caffeine is anti-inflammatory but other compounds in coffee stimulate

various aspects of the immune system. In a key 2016 study, researchers took blood samples from
volunteers before and after coffee, subjected the isolated blood cells to an inflammatory
stimulus, and measured the response of the cells. The authors summarize their surprising results
thusly: “Remarkably, the release of inflammation mediators IL-6, IL-8, GROA, CXCL2, CXCL5 as
well as PGA2, PGD2, prostaglandin E2 (PGE2), LTC4, LTE4, and 15S-HETE was significantly affected
after coffee consumption. While in several individuals coffee consumption or caffeine treatment
caused significant downregulation of most inflammation mediators, in other healthy individuals
exactly the opposite effects were observed.” This may explain why coffee consumption increases
risk of some autoimmune diseases (rheumatoid arthritis, type 1 diabetes, systemic lupus
erythematous) while decreasing risk of others (multiple sclerosis, primary sclerosing cholangi-
tis, Crohn’s disease and ulcerative colitis). In addition, coffee decreases absorption of levothy-
roxine in people with Hashimoto’s thyroiditis, reduces efficacy of methotrexate in rheumatoid
arthritis, and instant coffee is a gluten cross-reactor.

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 Genetics appear to influence whether or not coffee is helpful or harmful to autoimmune disease suffer-
ers. In recent studies, two genes have been linked with autoimmune disease and coffee tolerance.

NAT2 POLYMORPHISMS. The N-acetyltransferase 2 (NAT2) enzyme is involved in the

metabolism of xenobiotics (foreign substances that are ingested or otherwise make their way into our
bodies), including coffee. Specific polymorphisms lead to a slower degradation of toxic intermediate
molecules, which can worsen autoimmune disease. Indeed, people with the NAT2 mutation that leads
to slower coffee degradation may have increased risk for autoimmune disease.

HL A GENES. Another gene implicated in autoimmune disease is human leukocyte antigen

(HLA), which influences activity of helper T cells and regulatory T cells. One recent study demon-
strated that coffee consumption increases the risk of autoimmune diabetes of adulthood in people
with high-risk HLA genes (specifically those with DR4-DQ8, DR3/4, DR3/3, DR4/4, DR4/3-DQ8, and/or
DQA1*0501-DQB1*0201).

Additionally, habitual coffee consumption can magnify cortisol release in response to a psychological
stressor. For anyone with unmanaged stress, this is yet another reason to avoid coffee.

The bottom line is that coffee is still best eliminated in the initial phase of AIP implementation. It’s
worthwhile to note that none of the above problems with coffee apply to green and black tea however.
The AIP eliminates coffee but not all caffeine.

Nuts, Seeds and Spices

Nuts, seeds and spices are typically regarded as nutrient-dense, health-promoting foods.

For example, a mere 20 grams of tree nuts per day is associated with substantially
reduced risk (think 20-70%) of cardiovascular disease, cancer, neurodegenertative
disease, kidney disease, diabetes, infections, and mortality from respiratory disease.

Nut consumption is also known to decrease markers of inflammation, and there’s emerging evidence of
beneficial effects on oxidative stress, vascular reactivity, and hypertension. Even three 1-ounce servings
per week can lower all-cause mortality risk by a whopping 39%, meaning that eating nuts on a regular
basis both improves and extends lifespan.

Spices derived from berries, fruits and seeds are rich sources of antioxidant phytochemicals. For exam-
ple, allspice (the berry of Pimenta officinalis) contains several aromatic compounds, including cineole,
eugenol, alpha pinene, alpha terpene, and limonene. These antioxidant bioactive compounds also have
anti-inflammatory, anti-cancer, sedative, antiseptic, antiviral and antifungal properties. Cumin (the seed
of Cuminum cyminum) contains many beneficial antioxidant and anti-inflammatory bioactive com-
pounds, including various terpenes, phenols, flavonoids and alkaloids. It aids digestion by increasing

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 digestive enzyme activity and increasing the release of
bile from the gallbladder after eating. Cumin has also
been shown to promote weight loss, improve blood sug-
ar regulation, and lower LDL “bad” cholesterol.

In addition, nuts (especially walnuts, pista-

chios, almonds and chestnuts) have
been proven to benefit the gut microbiome
thanks to their prebiotic fiber content.

A number of well-designed studies have shown excep-

tional benefits from 1 to 2 ounces daily of walnuts, in
particular, upon the health and composition of intestinal
microbiota. Walnut enriched diets increase abundance
of key probiotic strains of bacteria (including Bifidobacteria, Lactobacillus, Ruminococcaceae, Faecali-
bacterium, Clostridium, Dialister, and Roseburia) while decreasing pathogenic strains. This microbiome
shift is associated with reduced inflammation and lower LDL cholesterol. In fact, researchers concluded
that the gut microbiota may play a direct role in some of the health benefits associated with walnuts!
Almonds, pistachios and chestnuts have been similarly studied and, while walnuts reign supreme when
it comes to microbiome health, these other nuts also all have proven benefits to microbiome composi-
tion and metabolite production.

However, nuts and seeds are also relatively concentrated sources of phytates. Phytate is the salt of
phytic acid—that is, it is phytic acid bound to a mineral. Because phytate is formed when phytic acid
binds to minerals—typically calcium, magnesium, iron, potassium, and zinc—these minerals are then
unavailable to be absorbed by the gut. Along with blocking mineral absorption, phytates also limit the
activity of a variety of digestive enzymes, including the proteases trypsin and pepsin, as well as amy-
lase and glucosidase. This means that high phytates can cause similar problems as the digestive enzyme
inhibitors in grains and legumes, namely causing intestinal inflammation. Nuts and seeds typically also
contain a large amount of omega-6 polyunsaturated fats. These concerns make a stronger argument for
limiting consumption rather than eliminating these foods. In fact, overall health benefits of nut
consumption do not continue to increase beyond about 20 grams per day, and there’s some evidence
that consuming large amounts of nuts daily can increase disease risk (at least for stroke).

The strongest argument against nuts and seeds in the elimination phase of the Autoimmune Protocol
is that, unfortunately, tree nuts are one of the most allergenic foods, with true allergies (meaning the
body produces IgE antibodies against proteins in nuts) estimated at about 1% of the total population and
scientific studies showing that IgG food intolerance to nuts and seeds may affect up to a whopping
60% of us.

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 The following is a compilation of data from four different studies, showing the highest frequency of
intolerance for various nuts and seeds.

Nuts and Seeds % at-risk people with IgG Abs

Almond 35

Brazil nut 23

Cashew 50

Pecan 38

Pistachio 60

Sesame seed 7

Sunflower seed 45

Walnut 7

Chocolate
Cocoa (cacao, or dark chocolate) increases growth of key probiotic Bifidobacteria and Lactobacilli in the
gut, while decreasing undesirable Bacteroides, Clostridium, and Staphylococcus species. This is thanks
to cocoa’s very high polyphenol content (polyphenols are well-known modulators of gut micro-
biome composition). For reference, fruits and vegetables
typically contain 200-300mg of polyphenols per 100g
serving.

A really high quality fresh-pressed olive oil may contain

300mg per quart. Dark chocolate contains a whopping
700-800mg per ounce! Interestingly, a 2016 paper used
cacao polyphenols in a mouse model of autoimmune
myocarditis and showed they were protective.

Unfortunately, cocoa doesn’t get an automatic pass on

the Autoimmune Protocol because of several studies
showing that cacao polyphenols suppress Th2 and in-
crease Th1 helper T cell activity, which may or may not
be helpful depending on the details of immune function
in each individual.

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 Chia
Pseudograins are the starchy seeds or fruits of broadleaf
plants—the most common of which are amaranth,
buckwheat, chia, and quinoa—whereas cereal grains are
the starchy seeds of grasses. Pseudograins definitely
provide more nutrition than grains, having good amounts
of vitamins B1, B2, B3, B6 and B9, magnesium, phospho-
rous, copper and manganese as well as fiber and some iron.
They also contain some antioxidant and anticancer
phytochemicals. However, buckwheat, amaranth and
quinoa are all also rich in problematic compounds,
including saponins and amylase-trypsin inhibitors, and
prolamins in both quinoa and amaranth are known
gluten cross-reactors.

Chia may be a different story however. It comes from a

different family than quinoa, buckwheat or amaranth and chia doesn’t appear to contain the prob-
lematic compounds identified in other pseudograins. Chia is particular high in calcium, phosphorus,
potassium, and magnesium, with moderate amounts of sodium, iron, zinc, vitamin B3, and vitamin C.
Chia contains between two and ten times more fiber than whole grains and a 3:1 ratio of omega-3s to
omega-6s. Chia also contains antioxidant phytochemicals including chlorogenic and caffeic acids, as
well as the flavonols myricetin, quercetin, and kaempferol.

The reason chia doesn’t get an automatic pass on the AIP is its high mucilage fiber content. Mucilage
fiber also modulates the immune system in complex and potentially detrimental ways for anyone
with autoimmune disease. In particular, some types of mucilage specifically stimulate either the Th1
immune response (like flaxseed) or the Th2 immune response (like the mucilage in natto, or fermented
soybeans). Because there are many unanswered questions about the impact of chia mucilage on im-
mune function, it is initially eliminated on the AIP.

Chia earns its early reintroduction status thanks to other research that points to beneficial and ther-
apeutic activity of mucilage fiber. Mucilage from cactus pads, for example, has been shown to act as
a prebiotic, enhancing the growth of Lactobacillus, increasing short-chain fatty acid production, and
reducing the population of harmful species of enterococci, enterobacteria, staphylococci, and clostrid-
ia. Mucilage-rich psyllium is often used to stimulate normal bowel function and absorb excess water
(making it useful for both constipation and mild diarrhea). Some mucilage-rich herbs can suppress the
blood sugar response to a glucose meal, due to a delay in glucose absorption from the intestinal mem-
brane. And, the addition of mucilage to a calorie-reduced diet has been shown to cause greater weight
loss and greater reductions in triglyceride and total cholesterol levels than diet alone (possibly due to
reduced intestinal absorption of bile acids).

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 Eggs
Eggs are one of the most allergenic foods, affecting
approximately 2–3% of the entire population (compared
to the approximately 6% of kids and 4% of adults who
have any food allergy). Intolerance to eggs also appears
to be fairly common; in one study in IBS patients, 57%
of participants tested positive for IgG antibodies against
eggs.

In addition, the lysozyme in egg whites are potentially

problematic. One of the main functions of the egg white
is to protect the yolk against microbial attack while the
embryo grows. One of the ways it achieves this worthy goal is through the activity of lysozyme.
Lysozyme is an enzyme (a glycoside hydrolases) that is very good at breaking down cell membrane
components of Gram-negative bacteria. In addition, lysozyme does a great job of transporting these
bacterial protein fragments across the gut barrier. Lysozyme works specifically and very quickly to
break apart peptidoglycans (a type of glycoprotein in bacterial membranes, especially Gram-negative
bacteria); it is very resistant to heat, and is stable in very acidic environments. Humans also produce
lysozyme as part of our normal defense against bacterial infections: it’s in our saliva, tears, and mucus
(including the mucus layers in the intestines). So, if we already make our own lysozyme, why is it a
problem in egg whites?

Lysozyme has the ability to form strong complexes with other proteins or protein fragments. This
means that lysozyme from egg whites typically passes through our digestive system in large complexes
with other egg white proteins. Many of the other proteins in egg whites are protease inhibitors, thus the
lysozyme and egg white protein complexes become resistant to our digestive enzymes. The egg white
protease inhibitors that are most likely to be bound to lysozyme are ovomucin and ovastatin, which are
trypsin inhibitors (trypsin is one of our main digestive enzymes); cystatin, which is a cysteine protease
inhibitor; and ovoinhibitor, which is a serine protease inhibitor. None of these inhibit the activity of
lysozyme. As the lysozyme complex travels, largely intact, through our gut, lysozyme can also bind
with bacterial proteins from the bacteria normally present in our digestive tract (like the Gram-negative
E. coli), adding it to the complex.

Lysozyme also has an unusual chemical property (it maintains a positive charge) that allows it to cross
through the enterocytes by electrostatic attraction to negatively charged glycoproteins (proteoglycans;
an important part of the glycocalyx layer) embedded in the enterocyte cell surface. Studies have con-
firmed that consumed lysozyme gets into the circulation (that is, circulates throughout the body via the
blood) even in healthy individuals (even in conjunction with food intake as opposed to taking isolated
lysozyme as a drug or supplement, although the amount that enters the circulation is lower). Absorp-
tion of pure egg white lysozyme by itself into the circulation is probably not hazardous (at least in the

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 quantities that you would get from a plate of scrambled eggs because very high amounts do cause kidney
damage). The problem is the other proteins piggybacking on lysozyme across the gut barrier: the “leak”
of other egg white proteins is the reason egg allergies are so common, and the high likelihood of bacte-
rial proteins leaking out is why eggs (especially the whites) cause difficulties for those with autoimmune
disease.

Egg yolk on the other hand is a rich source of vitamin A, vitamin D (if free-range or pasture-raised),
vitamin B3, vitamin B6, vitamin B9, vitamin B12, choline, phosphorous and selenium while also contain-
ing modest amounts of vitamin E, vitamin B1, calcium, iron and zinc. The rich yellow or orange color
comes from the presence of two antioxidant carotenoids, lutein and zeaxanthin. Contrary to decades of
dogma, the cholesterol in egg yolks won’t raise blood cholesterol, and in fact, 47% of the fats in egg yolks
are the ultra heart-healthy oleic acid. Eggs also contain phospholipids, known to improve cholesterol
(especially by supporting HDL), reduce blood pressure, improve vascular function and reduce inflamma-
tion—all good things when it comes to cardiovascular disease! Because egg yolks are much less likely to
be problematic (and contain such valuable nutrition), they should be reintroduced before egg white or
whole egg.

Grass-Fed and A2 Dairy

Grass-fed dairy is a very rich source of conjugated linoleic acid (CLA), linked with reduced risk of
cardiovascular disease, obesity, cancer, diabetes, osteoporosis and lower levels of inflammation. This
may be mediated through CLA’s benefits to gut microbiome composition, as it is also known to have a
prebiotic effect on Bacteroidetes/Prevotella and Akkermansia muciniphila. Grass-fed dairy is also a rich
source of vitamin A, vitamin D, vitamin K2 and butyric acid, all nutrients known to improve gut barrier
function and immune regulation.

However, cow’s milk proteins (casein, casomorphin, butyrophilin, whey) are also known gluten cross-
reactors, which means that those with gluten intolerance may produce antibodies against gluten that
also recognize dairy proteins. For these people, eating dairy is
essentially the same as eating gluten. Rates of lactose intol-
erance (the inability to fully digest lactose, the main sugar in
milk) vary widely based on ethnicity, ranging from 5% among
northern Europeans to over 90% in some Asian and African
populations. In fact, in the United States alone, somewhere
between 30 and 50 million people are lactose intolerant!
While lactose intolerance involves a reaction to milk sugar,
a true dairy allergy involves reactions to various proteins
in milk (including casein and whey). Epidemiological reports
of cow’s milk allergies (IgE antibody reactions to cow’s milk
proteins) range from between 1 and 17.5% in preschoolers, 1
and 13.% in children ages 5 to 16 years, and 1 to 4% in adults in
Western Countries. The prevalence of cow’s milk sensitivities

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 (IgA and IgG antibody reactions to cow’s milk proteins) is unknown, although one study of IBS patients
showed that a whopping 84% of participants tested positive for IgG antibodies against milk proteins.
That’s an excellent rationale for eliminating dairy and then carefully reintroducing it to see how your
body reacts.

A special note should be made regarding ghee, also known as clarified butter. Because the fats and fat-
soluble nutrients in dairy are very beneficial and because it is the sugars and proteins in dairy which
pose potential problems for autoimmune disease sufferer, pure dairy fat is a very compelling early intro-
duction. Whereas butter is 82% fat (18% proteins, sugars and water), ghee is 99.7% fat. Very importantly,
for people with allergy, intolerance or gluten cross-reactions to dairy proteins, even the trace proteins
in ghee can be a problem. In this case, cultured ghee may be preferable as it is fermented, which breaks
down the dairy proteins, prior to being clarified (note that some people do still react to cultured ghee,
which is why even cultured ghee is eliminated initially on the AIP). Dairy reintroductions would ideally
start with ghee (cultured is preferable) and then progress to butter if ghee is tolerated. From there, other
dairy products can be challenged one at a time.

Additionally, if reintroducing dairy, there there’s compelling reasons to choose A2 dairy,

which refers to the variant of β-casein contained within.
The second most abundant protein in milk is β-casein, and there are at least 12 different variants of this
one protein. The two most common variants are called A1 and A2 β-casein and it turns out that even
though these proteins are extremely similar, they have quite different effects on human health.

A1 β-casein is linked to atherosclerosis and ischemic heart disease (heart disease caused by blood clots),
and there is evidence that it triggers type 1 diabetes. It causes gastrointestinal inflammation including
activating Th2 cells which drive antibody formation (of particular concern for those with autoimmune
diseases) and causing histamine release plus it delays gut transit time. A1 β-casein can cause symptoms
resembling lactose intolerance (in one study A2 milk didn’t cause symptoms in people who thought they
were lactose intolerant) and there’s even evidence that it causes decreased cognitive processing speed
and accuracy (i.e., brain fog) in some people. These effects are largely attributable to a peptide product of
the digestion of A1 β-casein called β-casomorphin-7.

(This is analogous to many of the effects of gluten being attributable to specific gliadin peptides.) Fur-
thermore, there is evidence that A1 β-casein harms the gut microbiome, causing a decrease in short-
chain fatty acid production.

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 A2 β-casein doesn’t have these effects, however, probably because it doesn’t break down
into β-casomorphin-7 in our digestive tract. It’s quite possible that many, if not all,
of the potential problems with dairy consumption only apply to A1 dairy, although
more research is definitely needed. It remains unknown if A2 β-casein is a gluten
cross-reactive protein.

Most milk contains a mixture of A1 and A2 β-casein, and

the proportion between these two protein variants varies
by animal type, breed, herd, state or province, and even
country. Most dairy in the USA is from Holstein cows
and their milk contains mostly A1 β-casein. In contrast,
the following animals produce milk that contains either
mostly or completely A2 β-casein (meaning their milk
can be labeled as A2 dairy):

ºº Camel
Buffalo

ºº Donkey
ºº Goat
ºº Horse
ºº Llama
ºº Reindeer
ºº Sheep
ºº Yak
ºº Some cow breeds (Guernsey, Jersey, Asian)
ºº
Because of the variability in proportion of A1 and A2 β-casein variants even within the same breed of
cow, animals should be genetically tested to verify that their milk only contains A2 β-casein before it is
labeled as such.

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 TROUBLESHOOTING
It’s important to emphasize, that while the AIP is the most expedient diet and lifestyle intervention for
autoimmune disease, it does not replace the care of your physician and other healthcare professionals.
Instead, it should be seen as a complementary approach to healing, used in conjunction with a function-
al/integrative approach to health which may include judicious use of medications, supplements, and
alternative therapies.

How long should you follow the AIP before troubleshooting? While clinical trials are starting to catch
up with the collective experience of a few hundred thousand people in the AIP community, there are
not yet have estimates of how long it takes to see symptom alleviation or resolution after adopting the
Autoimmune Protocol for different autoimmune diseases. In a 2017 trial in patients with IBD, 73% were
in full clinical remission after a 6-week long gradual transition to the Autoimmune Protocol (following
the excellent SAD to AIP in Six program). In addition, patients showed continued improvement in quanti-
tative assessments of disease activity over an additional 5 weeks of maintenance.

From a mechanistic standpoint, it takes about 3 weeks for complete cell turnover of the gut epithelium
(at least, in the absence of celiac disease, which may delay healing of the gut epithelium); the gut micro-
biome can respond to diet and lifestyle changes in as little as a few days (and up to a about 6 weeks); and
immune regulation, once inputs to immune function are dialed in, can occur in as little as a few days.
This is why there are examples in the AIP community of a person with reactive arthritis getting out of a
wheelchair after 3 days of following the AIP or someone with severe psoriasis seeing complete resolu-
tion in 3 weeks. While this is not the typical experience, most people (at least anecdotally) begin to see
improvement within a couple of months of adopting the AIP.

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 So, how long do you bang your head against the
(hopefully proverbial) wall before calling in reinforce-
ments? The general rule of thumb is no more than 3
months. Sometimes the solution is persistence, but if
you’re facing some additional barrier to healing that can
not be easily addressed by diet and lifestyle alone, AIP-
ing harder isn’t going to be the answer. And you won’t
know which route to take until you investigate.

If you aren’t seeing the results you’re expecting, the first

troubleshooting step to take it to thoroughly reflect on
how well you are implementing the AIP. The reason most
often seems to be missing an important aspect of the
Autoimmune Protocol, most commonly: the nutrient-
density piece (not eating organ meats, seafood or enough
veggies; sometimes this is in the form of lack of food diversity too), the sleep piece, or the stress piece.
The best strategy here is to work with an AIP Certified Coach to hone in on your individual challenges
and develop a personalized solution.

There are circumstances in which additional dietary changes, supplements, or medications may be
necessary. If you aren’t seeing results with diet and lifestyle alone, here are a few other factors you
might consider looking at:

ºº the need for digestive support

poor sleep quality

ºº the need for organ support (liver, thyroid, gallbladder)

ºº HPA axis dysregulation (aka adrenal fatigue)
ºº hormone imbalance
ºº additional food sensitivities, allergies or intolerances
ºº persistent/underlying infection (virus, parasites, SIBO)
ºº gut dysbiosis requiring treatment (antimicrobials or prescription probiotics)
ºº severe nutritional deficiencies requiring supplementation
ºº environmental allergens
ºº toxin exposure (past or current)
ºº
ºº
mental health challenges (like PTSD)

Some of these are easily surmountable, but most require working with a functional or integrative
medicine practitioner, to diagnose and successfully address. This is what is called troubleshooting, i.e.,
figuring out what barriers to healing you may be faced with and finding a solution.

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 Vitamin D: Get Tested
Despite being referred to as a vitamin, vitamin D is actually a steroid hormone (also called calcitriol).
Vitamin D, which our bodies synthesize in response to sun exposure, controls the expression of more
than 200 genes and the proteins that those genes regulate. It is essential for mineral metabolism (it
regulates the absorption and transport of calcium, phosphorous, and magnesium) and for bone mineral-
ization and growth. It is also crucial for regulating several key components of the immune system,
including the formation of important antioxidants.

Very importantly, vitamin D has recently been shown to decrease inflammation

and may be critical in controlling autoimmune and inflammatory diseases.

Vitamin D is also involved in the biosynthesis of neurotrophic factors, regulating release of such
important hormones as serotonin (required not only for mental health but also for healthy digestion!).
Because it helps control cell growth, vitamin D is also essential for healing. In addition, it activates areas
of the brain responsible for biorhythms. Scientists continue to discover new ways in which vitamin D is
essential for human health; for example, it may help prevent cancer.

Research has shown that vitamin D helps regulate gastrointestinal inflammation and enhances gut
barrier function. Vitamin D also activates proteins important for detoxifying lithocholic acid (a
secondary bile acid that’s toxic for intestinal cells). One way vitamin D helps maintain the integrity
of the gut mucosal barrier is by enhancing the intercellular junctions that control gut permeability, as
well as reducing inflammatory cytokines like interleukin-8. And, people with higher levels of vitamin
D have been shown to have lower levels of the very inflammatory bacterial protein endotoxin in the
blood, possibly due to vitamin D’s ability to improve gut barrier integrity. Observational studies have
shown that people with higher levels of vitamin D are
less likely to develop IBD, especially Crohn’s disease.

The composition of our gut microbiome is also sensitive

to our vitamin D status. One study found that vitamin D
supplementation (at a dose of 980 IU per kg bodyweight
per week for four weeks, followed by another four weeks
of taking 490 IU per kg of bodyweight) significantly
reduced levels of Gammaproteobacteria, which includes
the most common opportunistic pathogens, while also
increasing the bacterial richness of the gut microbiome
(one of the signature features of a healthy microbiome!).
In addition, the supplementation protocol increased the
number of CD8+ T cells in the upper gastrointestinal
tract, pointing to a benefit for immunity. In people with

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 multiple sclerosis, high levels of serum vitamin D (above 40 ng/mL) are associated with greater levels
of Ruminococcaceae, which produce SCFAs and may help protect against MS-related inflammation. In
contrast, vitamin D deficiency is linked with gut dysbiosis and severe colitis. Additional research shows
vitamin D deficiency may contribute to metabolic syndrome by aggravating diet-induced imbalances in
the gut microbiome.

About 75% of Westerners are deficient in vitamin D. Optimal serum vitamin D levels are between 50 and
70 nanograms per milliliter (ng/mL). It’s important to ask your healthcare provider to test your levels. If
you’re deficient, it can be tough to get enough vitamin D3 from foods (natural sources include grass-fed
and pasture-raised meats and seafood), so consider supplementing with vitamin D3 (5,000 IU daily is a
standard dose to address deficiency) and recheck every three months to make sure you don’t overshoot
the mark. Vitamin D levels in excess of 100 ng/mL can also cause health problems.

Working 1-on-1 with an AIP Coach

An AIP Certified Coach is a practitioner who has received advanced training in addition to their base
certification on the science behind autoimmune diseases and the AIP as well as practical strategies for
helping clients implement dietary and lifestyle interventions to best affect healing and achieve higher
levels of wellness.

These health and wellness practitioners from across the globe each have their own stories of illness,
struggle and healing, their own inspirational context that led to their commitment to serve the auto-
immune community. Their overarching philosophy is that real health begins with eating REAL food
and adopting a lifestyle that is conducive to long-term health. At the same time, AIP Coaches recognize
the individual nature of each person’s body and the many paths to wellness. They are here to meet you
where you are and be your dedicated support in finding the correct approach for you.

AIP Coaches can provide you with personalized support for

all stages of your journey on the Autoimmune Protocol.
Working one-on-one with an AIP Certified Coach, you’ll be
able to clarify when you’re moving in the right direction and
receive guidance when you’re off course.

AIP Coaches work with the unique individuality of each

client by using assessment tools like questionnaires and food
journals. They make personalized plans for each client based
on their distinct needs—no one-size-fits-all approach! Their
method is flexible and adaptable to a wide variety of goals
and situations.

THE AUTOIMMUNE PROTOCOL

166 by Dr. Sarah Ballantyne, PhD
 If you are transitioning to the AIP, your AIP Coach can provide you with information,
motivation and accountability, supporting your customized transition plan with tangible
resources such as meal plans, shopping lists, lifestyle guides, and practical strategies for
fitting the AIP into your life.

Once you have fully adopted the AIP, your AIP coach can providing you with emotional support for
sustaining this protocol throughout the healing process. Not seeing the results you expected or dealing
with additional health challenges? Your AIP Coach can help you troubleshoot and refine your implemen-
tation so that you get the most out of the AIP. Your AIP Coach can also guide you through the reintroduc-
tion phase, creating an individualized plan for reintroduction priorities, helping you to identify subtle
indicators of reactions, and providing advice on handling unexpected severe food reactions. Have you
been riding the AIP rollercoaster? Your AIP Coach can help you identify and find solutions to your own
personal challenges to implementation and maintenance of the protocol. Just need your own personal
cheerleader? Yep, your AIP Coach can do that too.

Often, healing just means putting the right practices in place.

Your AIP Coach is your expert guide for doing so in a customized
way. They want to help you discover the true foundations of good
health and support you every step of the way! Your body can heal
itself—it just needs the right tools!

Each AIP Coach focuses their practice slightly differently, and

no matter what your health and wellness needs, you’ll find
support that’s right for you. Find an AIP Coach near you, or one
who works with clients long-distant, in the AIP Certified Coach
Directory: http://aipcertified.com/coach-directory/

167 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 WORKING WITH YOUR
DOCTOR
Sometimes you have to call in the reinforcements. When it comes to underlying health challenges that
can’t be addressed with diet and lifestyle modification alone, it’s important to take advantage of your
healthcare providers’ expertise. Just as a prescription can’t replace the benefits of eating healthy food,
even the best diet and lifestyle can’t replace your doctor—although hopefully you’ll need to see her
less frequently.

When it comes to medical expertise, you have a lot of choice, and you can work with several different
practitioners. Depending on your particular situation, you may avail yourself of a variety of conven-
tional and alternative healthcare providers, including your primary-care physician or a medical
specialist, naturopathic doctor, chiropractor, acupuncturist, therapist, physical therapist, massage
therapist, nurse practitioner, registered dietician, nutritionist, nutritional therapy practitioner, or
certified health coach, among others. These experts are part of your team, and each of them share your
main goal: for you to be the healthiest you can be. It’s important to be an informed patient (but please
don’t self-diagnose with Dr. Google before you even enter the exam room!) and your own patient
advocate, and to use medical interventions judiciously. For example, antibiotics can be a life-saving
medication, but their overuse has led to antibiotic-resistant strains of bacteria like MRSA. Take advan-
tage of modern medicine when it’s truly needed and practice preventive medicine the rest of the time .

Effective preventive medicine requires active collaboration between patient and

healthcare provider.

Preventitive Medicine
The goal of preventive medicine, as the name implies,
is to prevent the development of disease and disability
through promotion of healthy diet, lifestyle, behaviors,
and environment, as well as a strong community. Effec-
tive preventive medicine requires active collaboration
between patient and healthcare provider. Thorough
medical evaluation allows for identification of under-
lying health challenges so that they can be addressed,
boosting the efficacy of the patient’s healthy-living
efforts. The patient’s responsibility is to be self-moti-
vated to make healthy dayto- day choices.There are both

168 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 merits and drawbacks to various supplements, medications, surgeries, therapies, and other treat-
ments, depending on your specific situation, so it’s worthwhile to elaborate on the types of healthcare
professionals who best align with the autoimmune protocol: those who practice within the realm of
functional and integrative medicine. According to the Institute for Functional Medicine, functional
medicinepractitioners (MDs, DCs, NDs, physical therapists, and even nutritionists) “address the un-
derlying causes of disease using a systems-oriented approach” and seek to engage “both patient and
practitioner in a therapeutic partnership.”

The Academy of Integrative Health & Medicine has a similar definition of integrative medicine: “The
field of integrative health and medicine reaffirms the importance of the relationship between practi-
tioner and patient, focuses on the whole person, is informed by evidence, and makes use of all appro-
priate therapeutic approaches, healthcare professionals, and professions to achieve optimal health and
healing.”

Both integrative and functional medicine practitioners look for the root causes of disease (like food
sensitivities, nutrient deficiencies, gut dysbiosis, hormone dysregulation, persistent infection, and or-
gan dysfunction) and use multifaceted approaches (that encompass diet, lifestyle, supplements, botan-
icals,medications, and so on) to promote health. If you aren’t seeing the results you were expecting on
the autoimmune protocol, these practitioners can help you troubleshoot by identifying confounding
factors that are inhibiting immune regulation or healing.

Finding a Practicioner

Functional and integrative medicine practitioners are doctors or alternative healthcare

providers with supplemental training who specialize in diagnosing and treating the root
causes of disease. The various facets of the AIP, such as the importance of gut health and
nutrient density, are generally compatible with the philosophies of functional and integra-
tive medicine specialists. Beyond ordering a wider range of tests than many other healthcare
professionals would, functional and integrative medicine specialists often use botanicals and
herbal remedies instead of, or in conjunction with, pharmaceuticals for a more diverse
approach to disease management and prevention.

A few online directories can help you find a like-minded healthcare provider near you. Try:

ºº Re-FindHealth.com ºº FunctionalMedicine.org
PaleoPhysiciansNetwork.com a4m.com

ºº ºº

169 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Here are some questions you might wish to
ask a potential provider:

ºº
How would you describe your practice and general approach?

ºº symptoms?
Do you have experience treating my condition or diagnosing others with similar

ºº take insurance? Will my insurance cover at least part of the cost of treatment?
What are the costs of office visits and your most commonly recommended tests? Do you

ºº recommend dietary changes, herbals or botanicals, chiropractic adjustment, nutritional

What are your firstline treatment options upon diagnosis? Do you predominantly

supplementation, hormone replacement, and/or prescription medications?

ºº or do you rely on other assessment tools? What other diagnostic tools do you use, and what
Do you use laboratory studies (urine, stool, saliva, and/or blood tests to aid your diagnoses,

is the science that supports those diagnostic tools?

ºº practice who is available for after-hours phone calls?

How long are your standard office consultations and followups? Is there someone in your

If you’re working with a practitioner who is not covered by your health insurance, it’s worth asking
your primary-care physician to order some tests. While different doctors have different preferences
for annual checkup blood work, many doctors will order:

ºº Kidney panel
Serum ferritin
ºº Lipid panel
Complete blood count with differential

ºº Diabetes panel ºº Vitamin D

ºº Thyroid panel (usually partial) ºº
ºº
You can take a copy of your results to an alternative healthcare provider, and thus save some money
on testing.

Types of Medical Testing

When you start working with a functional or integrative medicine practitioner, you can expect to un-
dergo a wide range of tests that will provide your doctor with a complete picture of your health status.
You can expect the tests to fall under a variety of categories and include a collection of the following
(chosen based on your history and symptoms)

170 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MED I CA L HI STO R Y ADVAN CE D B IO MARK E R T E S T IN G PANELS

ºº the use of questionnaires ºº Cancer

Complete review of medical history, including Autoimmune disease

ºº Hormonal imbalances
ºº Medication review and screening for drug
Immunization status and updating, if needed
ºº Metabolic disorders
ºº interactions ºº
FU N CT IO NAL T E S T IN G
ºº (for example, colonoscopy or mammogram)
Preventive screening review and planning

ºº Comprehensive stool analysis

Autonomic nervous system testing

ºº lifestyle habits, cholesterol levels, and blood

Risk factor analysis (for example, looking at
ºº Food sensitivity and allergy testing
pressure to establish cardiovascular disease risk) ºº Functional nutritional testing
ºº Genetic testing for risk genes
PH YSI CA L EXA M INAT IO N ºº Hormone profiling (looking at how levels change
ºº (for example, vital signs)
Standard physical examination ºº or cycle over time)
ºº lems
Hydrogen/methane breath testing for digestive prob-
ºº Body composition analysis
Nutrition-focused physical assessment

ºº Colonoscopy ºº Salivary cortisol analysis

Red blood cell membrane fatty acid analysis

ºº Dermatologic screening exam ºº Urine organic acid analysis

ºº Electrocardiogram ºº
ºº Glaucoma and vision screening CO M M E RCIAL LAB O RATO RY T E S T I NG
ºº Grip strength test Advanced lipid profile
ºº Pap smear (for women) ºº Antibody testing for autoimmune conditions
ºº Screening audiometry ºº Complete blood count with differential
ºº Spirometry—FEV1 and FVC ºº Comprehensive metabolic profile
ºº ºº Glucose tolerance testing
S ELF- A DM I N I S T E R E D T E S TS ºº Heavy metal testing
ºº Hormone levels
ºº Colon transit time
Basal body temperature
ºº Inflammation/oxidation markers
ºº Resting heart rate or heart rate variability ºº Kidney function
ºº ºº Liver function
I MAG I N G ºº Metabolic markers
ºº Bone density testing
ABI index for peripheral vascular disease ºº Mineral/electrolyte analysis
ºº Carotid and abdominal aortic ºº Thyroid function
ºº Aneurysm screening ºº Vitamin D levels
ºº Coronary calcium scoring ºº Gluten antibodies and gluten
ºº Echocardiogram ºº Enteropathy
ºº Mammogram or thermography (for women) ºº Other testing as indicated by your medical
ºº Thyroid ultrasound ºº history or unique risk factors
ºº

171 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Yes, this list may seem overwhelming, and it’s true
that some doctors are a little test-happy—which is
especially frustrating if you’re paying out of pocket.
Have a conversation with your healthcare provider
about the reasoning behind any particular test and ask
whether any tests can wait until the results are
available from the first round of testing.

Depending on the test results, your functional or

integrative medicine practitioner may recommend
specific dietary or lifestyle changes. You might be
prescribed medication, but you might also be recom-
mended a regimen of nutritional supplements,
herbal remedies, or botanicals to address your health
challenges. Treatments like chelation therapy, IV
nutrition therapy, or detoxification regimens may be recommended. And chances are high that your
practitioner will be pleased to know that you’re implementing the autoimmune protocoL.

172 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 RECOMMENDED
AIP RESOURCES
The AIP Lecture Series
The Autoimmune Protocol Lecture Series is a 6-week video-
based, self-directed online course that will teach you the scientific
foundation for thediet and lifestyle tenets of the Autoimmune
Protocol. Think of this course as going to college for your health!

THE AIP LECTURE SERIES FEATURES:

ºº Dr. Sarah Ballantyne, PhD
42 video lectures (totaling 16 hours!), all taught by
LEARN MORE
ºº dozens of printable guides
action steps to help you go from theory to practice

ºº daily self-discovery exercises to reinforce and refine implementation

ºº an online forum to connect with other students and ask questions
ºº guided discussions in the online forum
ºº weekly FAQ videos by Dr. Sarah Ballantyne, PhD in the online forum
ºº recommended reading for every topic
ºº
ºº
interactive quizzes to test your knowledge

The Paleo Approach

The Paleo Approach is the New York Times bestselling complete guide to
using diet and lifestyle to manage autoimmune disease and other chronic ill-
nesses. With over 400 pages of scientific explanations of the why’s, what’s,
and how’s behind diet and lifestyle recommendations to help regulate the
immune system and provide the body with the opportunity to heal. This en-
cyclopedic resource also contains tons of practical information including tips
for transitions, working with your doctor, medical test and treatments that
might be helpful, troubleshooting, and when and how to reintroduce foods.
This book goes into scientific detail, while keeping explanations accessible
and fun to read, and includes over 1200 scientific references. This is the book
for people who want to understand the contemporary science behind how
the food we eat as well as how we live our daily lives together impact our
bodies to either promote health or facilitate disease.
LEARN MORE

173 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 The Paleo Approach Cookbook
The Paleo Approach Cookbook is the National bestselling
companion cookbook to The Paleo Approach! The Paleo Approach Cookbook is
over 400 pages and includes over 200 recipes, all strict autoimmune protocol
(AIP), and lots of resources (over 100 pages worth!) to help you be success-
ful in the kitchen while you tackle the diet recommendations in The Paleo
Approach. With such a huge number of recipes (that each include cook time,
prep time, servings, tips, variations, nutrition facts, FODMAP alerts), as well
as hundreds of recipe variations, there’s something for everyone! The Paleo
Approach Cookbook also includes a summary of the diet, cooking guides,
kitchen How-Tos, shopping lists, food storage guides, kitchen tool essentials,
cooking glossary of terms, time management strategies, how to read labels,
recipe Top Ten, alphabetical Yes-No-Maybe-So list of foods, 6 one-week meal
plans (two of which are low-FODMAP) and MORE! LEARN MORE

The Healing Kitchen

Achieving health through nutritious food choices has never been simpler nor
more delicious thanks to The Healing Kitchen! This cookbook makes healing
using the Autoimmune Protocol completely accessible to everyone, regard-
less of your budget, time limitations, or access to specialty grocers. Armed
with more than 175 budget-friendly, quick and easy recipes made with ev-
eryday ingredients, you get to minimize time and effort preparing healthful
foods without sacrificing flavor! Straightforward explanations and a com-
prehensive collection of visual guides will teach you which foods are the best
choices to mitigate chronic illnesses, including autoimmune disease. Real-life
practical tips on everything from cleaning out your pantry and easy ingre-
dient swaps to reinventing leftovers and DIY flavor combinations will help
you go from theory to practiceeffortlessly. Even better, twelve 1-week meal
plans with shopping lists takes all the guesswork out of your weekly trip to the
LEARN MORE
grocery store!

174 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Paleo Principles
Paleo Principles is the most comprehensive resource to date for those seek-
ing a scientifically founded nutritional approach to optimal health. In her
signature approachable yet scientifically detailed style, Dr. Sarah Ballantyne,
PhD, has laid a complete foundation for understanding the principles of the
Paleo template in order to inform and empower your day-to-day choices.
Combined with an unprecedented collection of practical strategies, tips, and
visual guides, plus more than 200 delicious recipes and twenty meal plans for
diverse health goals, this book is a one-stop-shop for nutrition nerd, health
nut, and gourmand alike. With the perfect balance of detailed explanations,
accessible summaries of actionable information, and visual guides, Paleo
LEARN MORE

175 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MORE RESOURCES
COAC HI N G H EA LT H T RACKERS
AIP Certified Coach directory Oura Ring
ºº ºº
SAD to AIP in Six
ºº H O M E T H ER A PIES
AIP Reset
ºº Joovv
ºº
PANT RY I N G R E D I E N T S,
S NAC K S A N D T R EAT S A IP CO O KB O O KS
The Paleo Approach Cookbook
ºº
One Stop Paleo Shop
ºº by Dr. Sarah Ballantyne, PhD
ShopAIP
ºº The Healing Kitchen
ºº
Thrive Market
ºº by Dr. Sarah Ballantyne, PhD
Sweet Apricity
ºº & Alaena Haber, OTC
Power Balls
ºº The Autoimmune Paleo Cookbook
ºº by Mickey Trescott, NTP
Epic Bars, Broth and Animal Fats
ºº
Tropical Traditions
ºº Alternative Autoimmune Cookbook
ºº by Angie Alt, NTC
M E AL D E L I V ERY
Nourish by Rachael Bryant
Paleo On The Go ºº
ºº Simple French Paleo
ºº by Sophie Van Tiggelen
M E AL PL A N N I N G
He Won’t Know It’s Paleo

ºº
Real Plans ºº by Bre’anna Emmitt
The Autoimmune Protocol Made Simple
Q UA L IT Y M E AT ºº by Sophie Van Tiggelen
ButcherBox
ºº The Nutrient-Dense Kitchen
ºº by Mickey Trescott, NTP
US Wellness Meats
ºº
GrassFed Traditions
ºº A IP B LO G G ERS, M EET-U PS
PastureBird
ºº & OT H ER R ESO URCES
FOOD-B A S E D S U PPL EM ENT S AIP Community

Vital Proteins Liver Pills

ºº
ºº
Vital Proteins Collagen Peptides
ºº
Vital Proteins Collagen Veggie Blend
ºº
Dr. Ron’s Ultra-Pure Organ Delight
ºº

176 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 PA R T F I V E

Meal Plans & Recipes

177 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 Meal Plan 1
BREAKFAST LUNCH DINNER

•• Sweet Italian Sausage •• Clam Chowder •• Mild Barbacoa

•• DIY Braised GreensB •• DIY Salad B •• Guacamole

Saturday
•• Berries Freeze half of the chowder for later •• Tortillas
••
in the week.
½
Replace to 1 pound of ground pork in the Lemon Parsley Caulirice
sausage mixture with liver, following instructions
Serve with shredded lettuce, chopped cilantro,
in “Sneaky Liver” Ground Beef. Make half of the
and fresh lime wedges.
sausage mix into small meatballs for soup. Make
enough DIY Braised Greens for 2 breakfasts.

•• DIY Soup B •• LEFTOVER Barbacoa, Guaca- •• Spatchcock Chicken

Use Sweet Italian Sausage meat balls, carrots,
celery, onion, spinach, and fresh parsley.
mole, Tortillas, Caulirice
•• Roasted Broccoli

Sunday
Make enough soup for three breakfasts. •• Celery Root Puree

•• LEFTOVER Sweet Italian •• Shrimp Salad •• LEFTOVER Barbacoa, Guaca-

Sausage mole, Tortillas, Caulirice
Monday •• DIY Braised Greens B
•• Berries

•• LEFTOVER DIY Soup •• DIY Salad B •• Gremolata-Topped Fish

•• LEFTOVER Clam Chowder Fillets
•• Tostones
Tuesday
•• Simple Fennel Salad

•• Sauerkraut •• LEFTOVER Spatchcock •• LEFTOVER Gremolata-Topped,

•• LEFTOVER Sweet Italian Sausage Chicken, Roasted Broccoli,

Celery Root Puree
Fish Fillets, Tostonees, Simple
Fennel Salad
and an orange
Wednesday

•• LEFTOVER DIY Soup •• DIY SaladB •• LEFTOVER Spatchcock

•• LEFTOVER Clam Chowder Chicken, Roasted Broccoli ,

Celery Root Puree
Thursday

•• DIY Braised GreensB •• DIY SaladB •• Broiled Pork Chops

•• LEFTOVER Sweet Italian •• LEFTOVER Clam Chowder •• Broiled Asparagus

Friday
Sausage, Barbacoa, or
Spatchcock Chicken
•• Maple and Sage Roasted
Winter Squash
•• Half a grapefruit

B = Recipe is located in Basics Section

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by Dr. Sarah Ballantyne, PhD
 Shopping List 1
MEAT •• celery - 6 stalks

•• bacon - 4 slices •• celery root - 2

•• beef shoulder or brisket – 5 to 7 pounds •• cilantro – 1 large bunch

•• whole chicken – 4 to 6 pounds •• fennel bulbs - 20 ounces

•• clams - 3 cans •• fresh basil - 3/4 teaspoon

•• duck fat - 3/4 cup •• fresh oregano - 2 tablespoons

•• fish fillets – 4 servings •• fresh parsley - 2 cups

•• ground pork - 3 pounds •• fresh rosemary - ½ teaspoon

•• pork chops - 2 pounds •• fresh sage - 1 tablespoon

•• precooked shrimp - 1 pound •• fresh thyme - 1 teaspoon plus 4 sprigs

•• garlic - 3 heads
FRUITS •• green plantains - 3

•• oranges - 2 •• onion - 2

•• mango - 1 •• red onion – 1 ½

•• limes - 5 •• romaine lettuce - 1 head

•• lemons - 7 •• spinach – 6 cups

•• green plantains - 3 •• turnip - 1

•• grapefruit -1 •• winter squash - 2 pounds

•• berries - 2 pounds •• Salad veggies of choice for DIY Salad – 4 meals

•• Greens of choice for DIY Braised Greens – 3 meals
DELI & PREPARED FOODS
•• Bone stock - 10 cups ( SPICES
or ingredients to make homemade) •• bay leaf
•• Beef Bone Stock – 4 cups •• cinnamon sticks - 2
(or ingredients to make homemade)
•• coarse sea salt
•• dried marjoram leaves
VINEGAR & OIL •• dried oregano
•• apple cider vinegar
•• dried rosemary
•• avocado oil
•• dried rubbed sage
•• coconut oil
•• dried savory
•• olive oil
•• dried tarragon
•• Ingredients for Salad Dressing of choice
•• dried thyme
•• garlic powder
VEGETABLES •• ground ginger
•• asparagus - 1 pound
•• ground turmeric
•• avocados - 3
•• onion powder
•• broccoli – 8 cups
•• sea salt
•• cabbage - 3 pounds (or storebought raw
•• truffle salt
sauerkraut)
•• carrot – 1 bunch
•• cauliflower - 1

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by Dr. Sarah Ballantyne, PhD
 SWEETENERS & BAKING SUPPLIES NONPERISHABLES
•• baking soda - ¹⁄8 teaspoon •• plantain chips - ¼ cup

•• blackstrap molasses - 1 tablespoon •• fish sauce - 5 tablespoons

•• cassava flour - 1 ½ cups •• Ingredients for Salad Dressing of choice

•• cream of tartar - ¼ teaspoon •• coconut cream - 2 cups

•• maple sugar - 2 tablespoons

MAKE AHEAD OR PURCHASE QUALIT Y OPTIONS

•• Salad Dressing of Choice
•• Bone Stock
•• Sauerkraut

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by Dr. Sarah Ballantyne, PhD
Meal Plan 2
BREAKFAST LUNCH DINNER

•• Breakfast Sausage •• DIY Baked Chicken Breast •• Meatloaf

•• Sauerkraut B
•• Asparagus Soup •• Mashed Plantain

Saturday
•• Mixed berries Make enough chicken for 4 meals
•• DIY Steamed VeggiesB
Make enough steamed veggies for
1 meal of leftovers

•• LEFTOVER Breakfast Sausage, •• Shaved Brussels Slaw with •• DIY Steamed VeggiesB
Steamed Veggies Apple and Mint
•• LEFTOVER Meatloaf, Mashed
•• Mixed Berries •• LEFTOVER Chicken Breast Plantain
Sunday

•• LEFTOVER Breakfast Sausage •• DIY Salad B •• LEFTOVER Shaved Brussels

•• Sauerkraut B
•• LEFTOVER Meatloaf Salad and Chicken
Monday •• A banana

•• LEFTOVER Asparagus Soup, •• LEFTOVER Shaved Brussels Salad, •• Hamburger Stew

Serve with lox DIY Chicken
•• DIY SaladB

Tuesday

•• LEFTOVER Hamburger Stew •• DIY SaladB •• Broiled Salmon

•• LEFTOVER Meatloaf, Mashed •• Lemon Parsley Caulirice
Wednesday Plantain
•• Asparagus Soup LEFTOVER

•• LEFTOVER Breakfast Sausage •• LEFTOVER Hamburger Stew •• Simple Fennel Salad

•• Sauerkraut B
•• LEFTOVER Broiled Salmon,

Thursday •• An orange Lemon Parsley Caulirice

•• LEFTOVER Breakfast Sausage •• LEFTOVER Hamburger Stew •• Shrimp Pad Thai

and Simple Fennel Salad

Friday

B = Recipe is located in Basics Section

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by Dr. Sarah Ballantyne, PhD
 Shopping List 2
MEAT/SEAFOOD •• carrots - 6

•• bacon - 6 ounces •• cauliflower – 1 ½ heads

•• chicken breasts - 4 pounds •• celery – 5 stalks

•• ground beef – 3 pounds •• chives – 1 tablespoon

•• ground pork – 4 pounds •• cilantro - 5 tablespoons

•• liver – 1 pound •• fennel - 1 pound

•• lox – 8 ounces •• fresh basil - 3 tablespoons

•• pancetta -4 ounces •• fresh oregano - 3 tablespoons

•• salad shrimp – 1 pound •• fresh parsley - ½ cup

•• salmon fillets – 4 servings •• fresh thyme 2 tablespoons plus 5 sprigs

•• garlic - 2 heads
FRUITS •• green onions - 5
•• apples (3) •• mint - 1/3 cup
•• oranges - 2 •• mushroom – 8 ounces
•• Granny Smith apple - 1 •• rosemary – 1 sprig
•• green plantains - 7 •• sage - 2 teaspoons
•• lemons - 3 •• white onion - 1
•• limes - 3 •• yellow onions - 2
•• bananas - 2 •• zucchinis - 2
•• berries, mixed – 1 pound •• Salad veggies of choice for DIY Salad – 3 meals
•• Veggies of choice for DIY Steamed Veggies – 3
NONPERISHABLES meals

•• apple cider vinegar

•• avocado oil SPICES
•• coconut oil •• bay leaf

•• coconut vinegar •• dried thyme

•• olive oil •• ground mace

•• Ingredients for Salad Dressing of choice •• ground ginger

•• coconut aminos - 3 tablespoons •• sea salt

•• coconut milk yogurt (optional) •• truffle salt (optional)

•• fish sauce - 4 tablespoons •• Ingredients for seasoning of choice

•• baking soda – ½ teaspoon •• Ingredients for Salad Dressing of choice

•• blackstrap molasses – 1 tablespoon

MAKE AHEAD OR PURCHASE
•• beef stock - 3 cups (or ingredients to make home-
made) QUALIT Y OPTIONS
•• chicken stock – 6 cups (or ingredients to make •• Salad Dressing of Choice
homemade) •• Bone Stock
•• Sauerkraut
VEGETABLES
•• asparagus -2 bunches
•• broccoli slaw – 1 (12oz) package
•• Brussels sprouts - 2 pounds
•• cabbages - 3 pounds (or raw sauerkraut)

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 Meal Plan 3
BREAKFAST LUNCH DINNER

•• Beef Heart Sausage •• Vegetable Soup with Chicken •• Greek-Inspired Lamb Chops
•• Applesauce Sausage
•• Mashed Acorn Squash with
•• DIY Steamed Vegetables B •• DIY SaladB Forty Cloves of Garlic
Saturday
•• Sauerkraut B •• DIY Braised GreensB
•• Cauliflower Rice

•• LEFTOVER Vegetable Soup •• LEFTOVER Greek-Inspired •• Roasted Chicken

with Chicken Sausage Lamb Chops, Mashed Acorn
•• Whole Carrot “Tabouleh”
•• DIY SaladB Squash with Forty Cloves of
•• Mint Pesto Zucchini “Pasta”
Sunday Garlic & Cauliflower Rice
and DIY Braised GreensB •• Roasted Radishes

•• LEFTOVER Beef Heart Sausage •• Steamed Clams •• Bacon- Braised Whitefish

•• Cinnamon Broiled Grapefruit •• LEFTOVER Mashed Acorn and Brussels
Monday •• DIY Steamed VegetablesB Squash with Forty Cloves of •• Garden Green Vichyssoise
Garlic, Mint Pesto Zucchini
•• SauerkrautB “Pasta” and Roasted Radishes

•• LEFTOVER Roasted Chicken •• LEFTOVER Steamed Clams , •• “Spaghetti”

and Applesauce Garden Green Vichyssoise
•• DIY Fruit Salad
•• DIY Steamed VegetablesB •• Sweet Potato Chips
•• DIY SaladB
Tuesday
•• SauerkrautB

•• LEFTOVER Beef Heart Sausage •• LEFTOVER Roasted Chicken, •• Salmon with Maître D’
or Apple Chicken Sausage, Fruit Salad, Whole Carrot “Butter”

Wednesday
Garden Green Vichyssoise “Tabouleh”
•• Savory Roasted Taro
•• Kale Chips
•• DIY Braised GeensB
•• Wild Mushrooms & Tarragon

•• Superfood Smoothie •• LEFTOVER Salmon with •• LEFTOVER Bacon -Braised

Maître D’ “Butter”, Fruit Salad, Whitefish and Brussels and
Kale Chips Wild Mushrooms and
Thursday
•• Easy Broiled Asparagus Tarragon

•• LEFTOVER Beef Heart Sausage, •• LEFTOVER “Spaghetti”, Sweet •• LEFTOVER Roasted Chicken,
Applesauce Potato Chips Savory Roasted Taro, Easy
•• DIY Steamed VegetablesB •• DIY SaladB Broiled Asparagus
Friday
•• SauerkrautB •• DIY Braised GreensB

B = Recipe is located in Basics Section

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 Shopping List 3
MEAT & SEAFOOD •• kohlrabi (½ cup)
•• bacon (8 oz.) •• leeks (4)
•• beef heart (3 lbs., ground preferred) •• mint (fresh)
•• ground beef (1 lb.) •• mushrooms (any type, ½ lb.)
•• ground chicken or turkey (4 lbs.) •• mushrooms (wild, 1 ½ lbs.)
•• ground lamb (1 lb.) •• onions (2)
•• ground pork (2 lbs.; or 1 lb. each ground •• oregano (fresh)
pork and pork fat)
•• parsley (fresh)
•• lamb chops (2 lbs.)
•• radishes (1 lb.)
•• whole chickens (2, 4–6 lbs. each)
•• spaghetti squash (1 large or 2 small)
•• Seafood
•• spinach (2 cups)
•• littleneck clams (4–5 lbs.)
•• sweet potatoes (1–2)
•• salmon (3-4 [6–8 oz.] fillets)
•• taro root (2 lbs.)
•• whitefish (1½–2 lbs.)
•• tarragon (fresh)
•• turnip (½ cup)
FRUITS •• zucchini (2 lbs.)
•• apples (4–5) •• greens for braising (for 4 meals)
•• avocados (4–5) •• leafy greens plus add-ons for salads (for 4 meals)
•• banana (1) •• leafy greens and superfood add-ons for Superfood
•• Granny Smith apples (2) Smoothie (for 1 meal)
•• grapefruit (1) •• seasonings for Cauliflower Rice (garlic, herbs,
•• ingredients for your favorite fruit salad
lemon, etc.)
(for 3 meals) •• veggies for steaming (for 4 meals)
•• lemons (4) •• Pantry Items
•• avocado oil
NONPERISHABLES
•• black olives (4 oz.) PL AN AHEAD
•• ingredients for your favorite salad dressing •• Apple-Chicken Sausage for Vegetable Soup:
(oil, vinegar, herbs, etc.) Either precook sausage patties or stuff sausage
•• raisins (2 tablespoons into casings and then parboil; let cool and then
freeze Applesauce

VEGETABLES •• Beef Heart Sausage: Either precook sausage pat-

••
ties
acorn squash (2 large)
or stuff sausage into casings and then parboil;
•• asparagus (1 lb.) let cool and then freeze
•• basil (fresh) •• Bone Stock
•• Brussels sprouts (1 lb.) •• Kale Chips
•• cabbage or other veggies for fermenting (3 lbs.) •• Maître D’ “Butter”
•• carrots with greens (2 lbs.) •• Poultry Seasoning for Roasted Chicken
•• cauliflower (2 heads) •• Salad Dressing
•• cilantro (fresh) •• Sauerkraut: Note that this needs to ferment,
•• dill (fresh) typically for a week
•• garlic (6–8 heads) •• Sweet Potato Chips
•• kale (2 bunches)

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Meal Plan 4
BREAKFAST LUNCH DINNER

•• Bacon Fruit Cups •• Bacon-Apple Chicken Burgers •• Teriyaki-Poached Trout

•• DIY SaladB with Maple-Cranberry Sauce
•• Cauliflower Rice
•• Roasted Butternut Squash
•• DIY Steamed VegetablesB
Saturday •• Roasted Broccoflower

•• LEFTOVER Bacon-Apple •• Tuna Salad Wrap •• Tarragon Roasted Pork

Chicken Burgers with Maple-
Cranberry Sauce and Roasted
•• Plantain Chips or Crackers •• LEFTOVER Roasted

Sunday Broccoflower •• “Cream” of Broccoli Soup Butternut Squash

•• DIY Braised GreensB
•• SauerkrautB

•• Superfood Smoothie •• LEFTOVER Teriyaki-Poached Trout •• 50/50/50 Burgers with

and Cauliflower Rice Portobello “Buns”
Monday •• DIY SaladB •• French Fries
•• Guacamole
•• Raw Veggies

•• LEFTOVER Bacon-Apple Chick- •• LEFTOVER Tarragon Roasted Pork •• Simple Grilled Steak with
en Burgers with Maple and Plantain Chips or Crackers Rhubarb Chutney
Cranberry Sauce and Roasted
•• DIY SaladB •• Roasted Sweet Potato
Tuesday Butternut Squash
•• DIY Steamed VegetablesB
•• DIY Steamed VegetablesB

•• LEFTOVER 50/50/50 Burgers •• LEFTOVER Tarragon Roasted Pork , •• Lemon and Thyme Broiled
•• Taro Hash French Fries, Guacamole Salmon with Blood

Wednesday •• •• Raw Veggies Orange Salsa

••
Sauerkraut
DIY SaladB
•• LEFTOVER “Cream” of
Broccoli Soup

•• Superfood Smoothie •• Sardine Salad •• Greek-Inspired Lamb

•• LEFTOVER Plantain Chips or Chops

Thursday Crackers •• Mint Pesto Zucchini

“Pasta”
•• LEFTOVER Roasted Sweet
Potato

•• LEFTOVER 50/50/50 Burgers •• LEFTOVER Greek-Inspired Lamb •• LEFTOVER Lemon and

and Taro Hash Chops, Mint Pesto Zucchini “Pasta” Thyme Broiled Salmon
and Roasted Sweet Potato with Blood Orange Salsa,
Friday “Cream” of Broccoli Soup
•• DIY Steamed VegetablesB

B = Recipe is located in Basics Section

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 Shopping List 4
MEAT •• green onion (1)

•• bacon (2 ½ lbs.) •• mint (fresh)

•• bison liver (1 lb.) •• onions (2)

•• ground beef (1 lb.) •• oregano (fresh)

•• ground chicken or turkey (2–2½ lbs.) •• parsley (fresh)

•• lamb chops (2 lbs.) •• plantains (2–4 green)

•• pork roast (4–5 lbs.) •• portobello mushroom caps (4–6)

•• steaks (2 [4–8 oz.]) •• red onion (1)

•• rhubarb (8 oz.)
SEAFOOD •• rosemary (fresh)
•• salmon (4–6 [6–8 oz.] fillets) •• sweet potatoes (2 lbs.)
•• trout (3–4 [6–8 oz.] fillets) •• taro root (1 lb.)
•• tarragon (fresh)
FRUITS •• thyme (fresh)
•• apples (3) •• zucchini (2 lbs.)
•• avocados (7) •• greens for braising (for 1 meal)
•• banana (1) •• large lettuce leaves (such as romaine or butterleaf)
•• berries, melon, or other fruit (1 cup for Bacon Fruit for Tuna Salad Wraps
Cups) •• leafy greens plus add-ons for salads (for 4 meals)
•• blood oranges (2 lbs.) •• leafy greens and superfood add-ons for Superfood
•• cranberries (2 cups, fresh or frozen) Smoothie (for 2 meals)

•• lemons (3–4) •• raw vegetables for dipping (2 meals)

•• limes (2–3) •• seasonings for Cauliflower Rice (garlic, herbs,

••
lemon, etc.)
orange (1)
•• starchy root vegetable for French Fries (1 lb.)

NONPERISHABLES •• veggies for steaming (for 4 meals)

•• albacore tuna (1 [5 oz.] can)

PANTRY ITEMS
•• sardines (2 [4 oz.] cans)
•• capers •• avocado oil

•• ingredients for your favorite salad dressing (oil, •• balsamic vinegar

vinegar, herbs, etc.) •• Bone Stock (4 cups, or ingredients to make ½
batch—page 110)

VEGETABLES •• cinnamon (ground)

•• arugula or mustard greens (6–10 cups) •• coconut aminos

•• broccoflower (4–5 heads, enough for 8 cups of •• coconut oil (extra-virgin)

florets and stems) •• coconut water vinegar
•• broccoli (2 lbs.) •• cloves (ground)
•• butternut squash (2 lbs.) •• garlic powder
•• cabbage or other veggies for fermenting (3 lbs.) •• lard
•• cauliflower (2 heads) •• lemon juice (or additional fresh lemons to make
•• celery (1 head or heart) your own)

•• cilantro (fresh) •• lime juice (or additional fresh limes to make your
own)
•• garlic (3 heads)
•• mace
•• ginger root

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 •• maple syrup (grade B) OTHER
•• olive oil (extra-virgin) •• casings for sausage (optional)
•• onion powder •• pickles (raw fermented, or ingredients to make
•• oregano (dried) your own)

•• protein powder for Superfood Smoothie •• sauerkraut (raw fermented, if not making your

••
own)
salt (pink or gray)
•• tallow, bacon fat, and/or duck fat •• vegetable juice (16–32 oz.)

•• tarragon (dried)
•• truffle salt (optional)
•• turmeric (ground)
•• white wine (½ cup) or more broth

PL AN AHEAD
•• Broth
•• Green Tea and Garlic Pickles for Tuna Salad Wraps—or you can buy pickles if you prefer
•• Plantain Chips or Crackers
•• Rhubarb Chutney
•• Salad Dressing
•• Sauerkraut (Note that this needs to ferment, typically for a week)
•• Steak Spice

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 BASICS

188 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 LARD AND TALLOW
PREP TIME COOK TIME SERVES
5 - 20 minutes 1 hour per pound of fat 1 pint tallow or lard per
pound of fat

1 to 5 pounds animal fat, ground or cut into 1-inch cubes

or smaller pieces

1. Place the fat in a large, heavy pot and cover with a lid. Place on the stovetop over low heat.
2. Stir every 30 to 45 minutes to dislodge any sticky bits from the bottom of the pot.
3. The tallow or lard is ready when all of the fat has melted (there will be some bits that look like
little bits of ground beef as well). This will take approximately 1 hour per pound of fat, varying
by type of fat and how small the pieces are.
4. Place a metal sieve over a glass bowl, measuring cup, or jar. Line with a single sheet of paper
towel. Pour the tallow through the lined sieve into the jar. Let cool before putting on the lid.
5. Store at room temperature out of direct sunlight for up to 3 months, or in the fridge or freezer
for long-term storage (up to 2 years).

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 BONE STOCK
PREP TIME COOK TIME SERVES
10 minutes 4 hours to 5 days 8 - 10 cups

CHICKEN OR TURKEY BEEF, BISON, LAMB, OR PORK

2 to 3 pounds chicken or turkey bones 2 to 3 pounds beef bones (or use bison,
(bones from 2 to 3 roasting chickens or lamb, or pork)
from 1 turkey); include giblets and feet if 1 gallon water (or enough to cover the
desired bones by 1 to 2 inches)
1 gallon water (or enough to cover the 1 tablespoon apple cider vinegar
bones by 1 to 2 inches)
2 medium yellow onions, roots cut off and
1 tablespoon apple cider vinegar quartered
2 medium yellow onions, roots cut off 3 bay leaves
and quartered
1 teaspoon whole cloves (omit for pork
4 to 5 carrots, cut in half stock)
6 to 8 celery stalks, cut into thirds 1 teaspoon salt
6 to 8 cloves garlic
3 bay leaves
1 teaspoon salt

1. Combine the bones, water, and vinegar in a large stockpot (or pressure cooker or slow cooker).
Bring to a boil over high heat and then reduce heat to maintain a simmer. Alternately, cook
under high pressure in a pressure cooker or bring to a boil then reduce heat to low in a slow
cooker.
2. During the first hour of cooking, skim off any foam that
has risen to the surface. (This improves the flavor of the
final stock.) You don’t need to do this step if you’re using
a pressure cooker.
3. Simmer, covered, for 24 to 48 hours (6 to 12 hours under
high pressure in a pressure cooker or 2 to 5 days in a
slow cooker). Periodically stir and check the water level.
Top up with additional water if needed to make sure the
ingredients are covered by an inch or two of water.
4. Add the remaining ingredients. Simmer an additional
4 to 6 hours (1 to 2 hours in a pressure cooker or 6 to 8
hours in a slow cooker).

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 5. Strain and discard the bones and vegetables. Store the stock in the fridge for up to 5 days or in
the freezer for up to 6 months.

FISH STOCK
2 to 4 pounds fish heads, tails, and bones
1 gallon water (or enough to cover the bones by 1 to 2 inches)
1 tablespoon apple cider vinegar
1 medium yellow onion or 2 medium leeks, roots cut off and quar-
tered
3 to 4 celery stalks, cut into thirds
1 to 2 carrots, cut in half
Optional: substitute 1 cup of water with white wine

1. Combine all the ingredients in a large stockpot (or pressure cooker or slow cooker). Bring to a
boil over high heat and then reduce the heat to maintain a simmer.
2. During the first hour of cooking, skim off any foam that has risen to the surface. (This im-
proves the flavor of the final stock.) You don’t need to do this step if you’re using a pressure
cooker.
3. Simmer, covered, for 3 to 4 hours (1 to 2 hours in a pressure cooker or 6 to 8 hours in a slow
cooker). Periodically stir and check the water level. Top up with additional water if needed
to make sure the ingredients are covered by an inch or two of water. Strain and discard the
bones and vegetables. Store the stock in the fridge for up to 5 days or in the freezer for up to 6
months.

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 COCONUT MILK
PREP TIME COOK TIME SERVES

5 minutes 1 hour (hands-on time is 1 ²⁄3 cups coconut milk

about 5 minutes)

2 cups finely shredded unsweetened dried coconut

2 3⁄4 cups water

1. Combine the coconut and water in a saucepan and bring to a full boil over high heat.
Turn off the heat, cover, and let sit for 1 hour.
2. Pour the coconut and water into a blender. Blend on high for 2 to 5 minutes (less time for a
high powered blender like a Blendtec or Vitamix, more time for other blenders), until the
texture is thick and only slightly granular (place a tea towel or other cloth over the lid of the
blender, and make sure to keep your hand over the top while the blender is running).
3. Pour the pulp into a nut-milk bag, yogurt-cheese bag, paint-straining bag, or fine-mesh
strainer suspended over a glass bowl, mason jar, or measuring cup. (If using a nut-milk bag or
paint-straining bag, it is easier to handle if you place the bag inside a sieve or strainer.)
4. Either let the coconut milk strain out by gravity or squeeze the pulp through the nut-milk bag.
5. If not using immediately, store the coconut milk in a glass jar in the fridge for up to 2 weeks
or in the freezer for up to 1 year. Shake well, blend, or gently warm before using.

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 COCONUT MILK YOGURT
PREP TIME COOK TIME SERVES

5 minutes (+ incubation none 1 3⁄4 cups

and chilling time)

1 ¾ cups homemade Coconut Milk or 1 (13½-ounce) can full-fat

coconut milk
1 ¼ teaspoon gelatin
2 teaspoons honey
Lactobacillus-based probiotic supplement, 15 to 20 billion PFU
(aka CFU)

1. Thoroughly clean or sterilize the jars of a yogurt maker, or the jars you’ll be using to make
the yogurt.
2. Pour the coconut milk into a heatproof glass container, if planning to heat the milk in the
microwave, or into saucepan, if planning to heat the milk on the stovetop. Sprinkle the gelatin
over the surface and wait 2 to 3 minutes for the gelatin to bloom (this just means the gelatin is
absorbing liquid). Stir in the gelatin.
3. Heat the coconut milk to 120°F in the microwave or on the stovetop (If you make this yogurt
frequently, you’ll quickly find out just how many seconds in your microwave heats the milk
perfectly—in my microwave, it’s 75 seconds.)
4. Stir thoroughly to make sure the gelatin is dissolved.
5. Let the milk cool to 105°F. (Anywhere between 100°F and 110°F will work, but don’t add your
probiotic until the coconut milk is below 110°F).
6. Stir in the honey. Open the probiotic capsule(s) and sprinkle
the contents into the milk. Stir well.
7. Pour into the sterilized jar(s) and incubate for approximate-
ly 12 hours (if the yogurt is too sour, incubate for a shorter
period of time next time; if it’s not sour enough, incubate for
longer).
8. Refrigerate the yogurt until the gelatin has set (2 to 3 hours).
Stir and enjoy!

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 KOMBUCHA
PREP TIME COOK TIME SERVES

20 mins + 14-17 days to none 4-6 servings

ferment, 10 mins for
2nd ferment

5 black or green tea bags (or about 5 teaspoons loose leaf tea)
¾ cups sugar
1 kombucha scoby
½ cup of previous batch of kombucha tea

1. Pour boiling water over teabags in a large teapot (make 4-6 cups of tea).
2. Steep tea for about 20 minutes, then stir in sugar until dissolved.
3. Allow tea to cool to room temperature. Remove tea bags or pour tea through a sieve to remove
leaves.
4. Place tea in a ½ gallon jar. Place scoby in the tea (it’s okay if it sinks, it will typically float up in
a couple of days). Add the ½ cup of the previous batch of kombucha tea to the jar (this helps get
the culture going more quickly). Top with room temperature filtered water until just before
the jar narrows at the top.
5. Cover with cheesecloth, muslin or paper towel held on
with a rubber band.
6. Allow to ferment for 14-17 days.
7. You may optionally do a second fermentation to flavor
your kombucha. Up to 3 tablespoons of flavoring liq-
uids like lemon juice, ginger juice, and fruit juices can
all be added to kombucha in 12 to 16oz bottles. Sliced
fresh ginger and fruits can also be added. To do this,
remove the kombucha scoby from the jar with clean
hands and start a new culture (remembering to reserve
½ cup of this batch of kombucha to add to the new
batch). Stir the kombucha and then pour into prepared
bottles with preferred flavorings. Tighten the caps on
the bottles and allow to ferment for 3-5 days.
8. Place in the fridge until you are ready to enjoy!

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 SAUERKRAUT
PREP TIME COOK TIME SERVES

20 mins - 1 hour 5 days - 5 weeks 30+ servings

3 pounds cabbage (1 large head or 2 smaller heads)

4½ tablespoons unrefined sea salt, pink, pickling, or other non
iodized salt

1. Peel a few of the outer leaves from each head and set aside.
2. Slice the cabbage as thinly as possible using a food processor, mandoline slicer, or a knife.
3. Place the cabbage into a large bowl (if you don’t have a bowl big enough for all 3 pounds, you
can do this in batches). Sprinkle with the salt.
4. Massage the cabbage with your hands to thoroughly distribute the salt and start the process of
breaking down the cabbage. Massage until well wilted.
5. Make sure your fermentation vessel is very clean (see note above for vessel recommenda-
tions). Pack the sauerkraut into the vessel, handful by handful, pressing down firmly with each
handful to make sure it’s tightly packed.
6. Place the large outer leaves over the top of the shredded cabbage (you may have to tear or
fold to be able to cover the entire surface). This ensures that the shredded cabbage stays
submerged.
7. Weigh down the cabbage. A clean glass jar slightly smaller in
diameter than the mouth of your fermentation vessel filled
with water works well. If you are using a fermentation crock,
use the weight that comes with it.
8. Cover with a breathable barrier (paint-straining bag, nut-milk
bag, several layers of cheesecloth, coffee filter, linen towel, or
even paper towels), making sure to secure with a rubber band
(unless using something like a paint-straining bag that has an
elastic around the opening). If using a fermentation crock, put
on the lid.
9. Check the level of the liquid above the surface of the cabbage
over the next 24 hours. If it is not at least 1 inch above the top
of the cabbage, dissolve 1 teaspoon of salt into 1 cup of water.
Then, pour the salty water into your fermentation vessel until
the level of the level of the water is at least 1 inch above the
top of the cabbage.

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 10. The sauerkraut will be ready in as little as 5 days, but can ferment for up to 5 months (check the liq-
uid level periodically and top up with salted water if needed). A little bubbling or foaming is normal.
11. Once the sauerkraut is fermented to your liking, transfer to smaller jars (if desired) and keep in the
fridge for up to 6 months.

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 GREEN TEA
AND GARLIC PICKLES
PREP TIME COOK TIME SERVES

20 minutes 3 - 5 days sliced, 30+ servings

6- 10 days whole

6 teabags green tea or 6 teaspoons loose-leaf green tea

¼ cup unrefined sea salt, pink salt, pickling salt, or other
noniodized salt
6 cups hot water (see Tips)
2 pounds pickling cucumbers
1 head garlic
2 sprigs fresh dill

1. Put the teabags and salt in a heatproof bowl. Pour the hot water over the teabags and salt.
Stir occasionally to make sure that the salt dissolves. Let cool to room temperature.

2. Slice the cucumbers ¼ inch thick (or slice into wedges or leave whole). Peel the garlic and leave the
cloves whole. Mix the cucumbers and garlic together.
3. Place the dill at the bottom of a large glass jar or fermentation crock. Pile the garlic and
cucumbers on top. Pour the cooled green tea over the top.
4. Place a glass jar, bowl, or the weight from your fermenta-
tion crock over the top of the cucumbers to keep them
submerged. There should be at least 1 inch of liquid above
the top of the cucumbers.
5. Cover with a breathable barrier (paint-straining bag,
nutmilk bag, several layers of cheesecloth, coffee filter,
linen towel, or even paper towels) and secure with a
rubber band (unless using something like a paint-straining
bag that has elastic around the opening). If using a
fermentation crock, put on the lid.
6. The pickles will be ready in 3 to 5 days if sliced, and 4 to 10
days if wedged or whole. After 3 days, taste them to see
7. if they are to your liking (they will soften as they get more
sour). Transfer to smaller jars (if desired) and keep in the
fridge for up to 2 months.

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 TIPS:
1. Green tea is traditionally made with water at 170°F to 185°F (as opposed to black tea, which is
made with boiling water). Bring the water to a boil, remove it from the heat, and then let it sit
for 1 to 2 minutes before pouring over the teabags.
2. The longer you ferment your pickles, the more sour and soft they will be. After 3 days, taste
every day, and move them to the fridge once they are to your liking.
3. Keep the garlic! Yes, it’s potent, but it’s delicious to use in Salad Dressings!

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 SALAD DRESSING
PREP TIME COOK TIME SERVES

5 to 10 minutes - 2 - 8 servings

BASIC VINAIGRETTE ITALIAN VINAIGRETTE

3 tablespoons oil, such as extra-virgin olive 6 tablespoons extra-virgin olive oil
oil or avocado oil
¼ cup apple cider vinegar
2 tablespoons acidic liquid
(such as fresh lemon juice, fresh lime ¼ teaspoon dried oregano leaves
juice, apple cider vinegar, balsamic ¼ teaspoon dried rosemary
vinegar, coconut water vinegar,
or white or red wine vinegar) ¼ teaspoon dried marjoram leaves
Pinch of salt ¼ teaspoon dried thyme leaves
¼ teaspoon dried savory
GREEK SALAD DRESSING
1 clove garlic, crushed
¼ cup fresh lime juice
Pinch of salt
2 tablespoons fish sauce
½ teaspoon honey
CREAMY BALSAMIC DRESSING
1 garlic clove, crushed
¼ cup extra-virgin olive oil
2 tablespoons chopped fresh cilantro
½ cup balsamic vinegar
1 tablespoon chopped fresh mint
¼ medium avocado
Pinch of salt or truffle salt
GREEK SALAD DRESSING
½ cup extra-virgin olive oil
2 tablespoons fresh lemon juice
¹⁄3 cup apple cider vinegar or red
wine vinegar
1 teaspoon dried oregano leaves
2 cloves garlic, crushed
1 teaspoon grated lemon zest
¹⁄8 teaspoon salt

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 1. Combine the ingredients in a blender. (If making the Basic Vinaigrette, simply combine the
ingredients in a jar shake before serving).
2. Blend in a blender until fully combined.
3. Store in the fridge and warm to room temperature before serving (just take it out of the fridge
about 30 minutes before meal time). Creamy Balsamic Vinaigrette and Thai Salad Dressing will
keep 3 to 4 days. The other dressings will keep for about a month.

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 HANDY-DANDY
SPICE BLENDS
GARLIC SALT HERBES DE PROVENCE
( M A K E S 6 TA B L E S P O O N S ) ( M A K E S 10 TA B L E S P O O N S )
¼ cup garlic powder 3 tablespoons dried marjoram leaves
2 tablespoons pink or gray salt or 3 tablespoons dried thyme leaves
truffle salt
3 tablespoons dried savory
GREEK SEASONING 1 teaspoon dried oregano leaves
( M A K E S 6 TA B L E S P O O N S ) 1 teaspoon dried rosemary
2 tablespoons dried lemon zest 1 teaspoon dried tarragon
2 tablespoons dried oregano leaves ½ teaspoon dried rubbed sage
2 tablespoons garlic powder
POULTRY SEASONING
( M A K E S 10 TA B L E S P O O N S )
ITALIAN SEASONING
( M A K E S 6 TA B L E S P O O N S ) 3 tablespoons garlic powder
1 tablespoon dried oregano leaves 3 tablespoons dried savory
1 tablespoon dried rosemary 2 tablespoons dried thyme leaves
1 tablespoon dried marjoram leaves 1 tablespoon dried marjoram leaves
1 tablespoon dried thyme leaves 1 tablespoon onion powder
1 tablespoon dried savory
1 tablespoon garlic powder TARRAGON SALT
( M A K E S 6 TA B L E S P O O N S )

STEAK SPICE ¼ cup dried tarragon, ground to a powder

( M A K E S 5 TA B L E S P O O N S )
2 tablespoons pink or gray salt or truffle salt
3 tablespoons truffle salt
1 tablespoon ground turmeric
1 teaspoon garlic powder 1. Combine the spices in a spice grinder or mini food

1 teaspoon onion powder processor and process until powdered, or place them
directly in a spice shaker or spice jar. If you don’t
1 teaspoon dried oregano leaves
have a spice shaker, you can also sprinkle by hand or
dust with a sieve. Store in the pantry or cupboard for
up to 6 months or freeze for up to 2 years.

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 DIY SALAD
PREP TIME COOK TIME SERVES

5 - 10 minutes none varies

L E A F Y G R E E N S (arugula, baby collards, beet greens, broccoli leaves,

cabbage, carrot tops, celery leaves, chard, endive, kale, kohlrabi greens,
lettuce, mizuna, mustard greens, pea leaves, radicchio, radish tops, sorrel,
spinach, sweet potato leaves, turnip greens, watercress)
V E G G I E S (asparagus [raw, broiled, grilled], avocado, beets [raw, roasted,
steamed], broccoli florets [raw or steamed], broccoli slaw, carrots [sliced,
shredded], celery root, cucumber, fennel, jicama, kelp noodles, kohlrabi,
microgreens, mushrooms, olives, onion, radish sprouts, radishes, sea vegeta-
bles, seaweed , sunflower sprouts, turnips, wakame noodles, zucchini and other
summer squash), optional
F R E S H H E R B S (basil, chervil, chives, cilantro, dill, fennel, mint, oregano,
parsley, tarragon), optional
F R E S H O R D R I E D F R U I T (apple, apricot, asian pear, citrus segments,
fresh figs, halved grapes, mango, melon, pear, pomegranate seeds, peaches,
raisins, dried cranberries, dried apricots), optional
P R O T E I N (bacon bits, shrimps, salmon, tuna, scallops, sliced steak, leftover
chicken, sliced leftover sausage), optional
SALAD DRESSING OF CHOICE

1. Combine your favorites from the lists above. Toss leafy

greens with veggies, herbs, and fruit, if using.
2. Add protein, if using.
3. Drizzle with salad dressing immediately before serving.

TIPS:
1. Toasted Coconut. Preheat oven to 325°F. Spread unsweetened
coconut flakes on a rimmed baking sheet. Bake 5 to 10 minutes,
until fragrant and turning golden brown.
2. When purchasing unsweetened banana chips or plantain chips,
be sure to read the ingredients label to verify that no sugar
or preservatives has been added and that they are cooked in a
healthy fat.

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 DIY SOUP
PREP TIME COOK TIME SERVES

10 minutes 15-20 minutes varies

2 parts Bone Stock

1 part leftover or precooked meat, cut into bitesize pieces
(chicken, pork, beef, lamb, sausage),
2 to 3 parts mixed vegetables, cut into bitesize pieces
(onion, celery, carrots, turnips, rutabaga, radishes, kohlrabi, leeks,
broccoli, seaweed, parsnip, green plantain, cauliflower, winter squash,
mushrooms, zucchini, sweet potato, spinach, kale, collard greens)
Fresh herbs (thyme, rosemary, sage, garlic, ginger, oregano, basil,
parsley, chives), optional
Salt, to taste

1. Bring stock to a simmer over medium heat on the stovetop.

2. Add the vegetables. If you have leafy greens or seaweed, add those at the same time as your
meat. If adding a tough fresh herb like rosemary or thyme, add now, otherwise, add with leafy
greens and meat.
3. Once the veggies are cooked to your liking (usually 10 to 15 minutes), add the meat, any leafy
greens, tender herbs or seaweed. Cook 2-3 more minutes.
4. Taste and add salt if needed. Enjoy!

GREAT COMBINATIONS
CHICKEN VEGETABLE SOUP: chicken bone stock, leftover chicken,
carrots, celery, onion, sweet potato, fresh parsley

STEAK AND POTATO SOUP: beef bone stock, leftover roast beef or
steak, carrots, celery, onion, mushrooms, potato or green plantain or
parsnip, rosemary, thyme

ASIAN CHICKEN SOUP: chicken bone stock, leftover chicken, carrots,

snap peas, bamboo shoots or water chestnuts, shitake mushrooms,
grated fresh ginger, and seaweed

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 PORK VEGETABLE SOUP: pork bone stock, leftover pork roast or chop, carrots, celery, onion, winter
squash, kale, canned tomatoes, crushed garlic, Italian seasoning mix (page tk)

SAUSAGE AND BROCCOLI SOUP: chicken or pork bone stock, leftover sausage, broccoli, onion, car-
rots, green plantain, a splash of white wine, thyme

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 DIY STEAMED VEGGIES
PREP TIME COOK TIME SERVES

5 to 10 minutes 3 to 40 minutes varies

Vegetable(s) of choice

ARTICHOKE: 35 to 40 minutes for whole artichoke, 20 minutes for baby artichoke, 10

minutes for artichoke hearts
ASPARAGUS: 4 minutes for thin spears, add an extra minute or two for thicker spears
BEETS: 30 to 40 minutes for whole medium sized, or wedges of larger beets
BROCCOLI: 5 minutes for florets, add an extra minute or two if florets are large
BRUSSELS SPROUTS: 10 to 12 minutes for whole, 7 to 8 minutes if cut in half
CABBAGE: 20 to 23 minutes for quartered, 8 to 10 minutes for shredded
CARROTS: 8 minutes for ¼-inch-thick rounds
CAULIFLOWER: 6 to 8 minutes for medium florets
KOHLRABI: 30 to 35 minutes for wedges
LEAF Y GREENS: 3 to 5 minutes, just until wilted
TURNIPS: 15 minutes for ¼-inch-thick slices
WINTER SQUASH: 5 to 10 minutes for 1-inch pieces
ZUCCHINI AND OTHER SUMMER SQUASH: 8 to 10 minutes for
¼-inch-thick slices, 15 to 20 minutes for whole pattypan squash

1. ill a saucepan with enough water so that the water just barely
F
reaches the bottom of the steamer insert or steamer basket.
2. eat over high heat. Once the water comes to a boil, add the
H
vegetables to the steamer insert or basket. Cover the saucepan
with a loose-fitting lid. If using a steamer insert, position the
lid so that one side hangs over the insert just enough to let the
steam escape.
3. ook until desired tenderness is reached, using the cooking
C
times above as a guide.

TIPS:
4. Adding a tablespoon of lemon juice, white wine vinegar, or
coconut water vinegar to the water under the steamer basket
will help retain nutrients in your vegetables.

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 5. Don’t have a steamer insert or a steamer basket? You can also “steam” vegetables by adding
about 1/2 inch of salted water to the bottom of a sauce pot, placing the vegetables in the water
once it comes to a boil (you can add lemon juice or vinegar, too), and covering the pan with a lid.

6. If you plan on using the microwave, cook times are typically a few minutes longer, depend-
ing on the wattage of your microwave. Simply rinse your vegetables and place in a micro-
wave-safe container with a vented lid, or a loose-fitting lid that you can leave a little open at
one corner (and no additional water other than what clings to your veggies after rinsing).

7. To steam frozen vegetables, the cook times are usually a bit shorter but check the packaging
for directions.

206 THE AUTOIMMUNE PROTOCOL

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 DIY BRAISED GREENS
PREP TIME COOK TIME SERVES

5 - 10 minutes 3 - 15 minutes 2- 4 servings

4 to 12 cups chopped greens (less for substantial greens and more

for tender greens)
2 tablespoons cooking fat (olive oil, ghee, butter, avocado oil, coconut oil,
tallow, lard)
1 tablespoon to 2 cups Bone Stock
salt, to taste

1. Heat the fat in a large skillet or wok over medium-high heat. Add the greens and 1 to 3 table-
spoons of the liquid, adding less for tender greens, more for tougher greens. Stir relatively
frequently. If the liquid evaporates before the greens are fully cooked, add a little bit more. For
tender greens, you probably won’t have to add more liquid. For tougher greens, you may need
to add additional liquid several times during the cooking time.
2. When the greens are done to your liking, taste and season with salt if desired then serve. Ide-
ally, this will be just as the liquid is fully evaporated. Otherwise, you can serve with tongs or a
slotted spoon to leave the liquid in the pan.
TIPS:
You can keep braised greens super simple or you can play with a
dding herbs and other seasoning. Crushed garlic, grated ginger, and
citrus zest should be added with the greens (if cooking very tender
greens, you may even want to add garlic and ginger to the oil for 1
to 2 minutes before adding the greens). Woody herbs like rosemary,
thyme, and savory can also be added with the greens. Tender herbs
like cilantro, parsley, tarragon, marjoram, basil, oregano, chives, and
green onion can be added right at the end of the cooking time.
1. he more tender the greens, the less time they take to
T
braise. Very tender greens that might also be used as salad
greens, like spinach, lamb’s quarter, sorrel, mizuna, sweet
potato greens, and celery leaves, cook very quickly—as little
as 3 to 4 minutes.
2. Mustard greens, turnip greens, radish tops, carrot tops, baby
collards, beet greens, kohlrabi greens, chard, and some more
tender varieties of kale are more substantial greens and take
longer to braise—5 to 10 minutes.

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 3. he greens that take the longest to cook are those with the thickest and most substantial leaves,
T
such as cabbage, kale, bok choy, broccoli leaves, cauliflower leaves, Brussels sprouts, and collards,
which more typically take 10 to 15 minutes to braise. The longer the cooking time, the more stock is
typically used.
4. s a general rule of thumb, the more tender the greens, the more the greens will shrink during
A
cooking. So, for tender greens like spinach, you’ll want to start out with more leaves. If cooking a
large amount of a tougher green, use 3 to 4 tablespoons of cooking fat and be prepared to use as
much as 2 cups of liquid.
5. If using a tougher green, remove stems before cooking.

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“SNEAKY LIVER” GROUND BEEF
PREP TIME COOK TIME SERVES

- 5 pounds ground meat

10 minutes

1 pound liver, frozen

4 pounds ground beef, thawed

1. Place frozen liver in the fridge for one hour to soften slightly but not thaw. Grate the mostly
frozen liver using a box grater.
2. Mix grated liver thoroughly with the ground beef.
3. Divide the ground meat into five 1-pound balls.
4. efreeze the meat by placing in freezer-safe container or bag and store for up to 3 months;
R
otherwise, use immediately.

TIPS:
1. Use in place of ground beef for any recipe.

209 THE AUTOIMMUNE PROTOCOL

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 AIP DINNER ROLLS
PREP TIME COOK TIME SERVES

15 minutes 25 minutes 6 rolls

1 ½ cup chopped green plantain (about 1 medium)

1/4 cup extra virgin olive oil
½ teaspoon salt
¹⁄3 cup coconut milk (or substitute with ¼ cup water
and an additional tablespoon olive oil)
1 cup cassava flour

1. Preheat oven to 425F.

2. Combine plantain, olive oil, salt and coconut milk in a blender and blend on high for 1-2
minutes, until a completely smooth puree.
3. Invert puree into a mixing bowl. Add cassava our and work into the puree until a sticky rm
dough forms.
4. Divide dough into six and roll each part into a ball (about 2” in diameter). Place on a baking
sheet. If desired, cut an ‘X’ with a sharp knife about ¼ “ deep at the top of each dough ball.
5. Bake for 25 minutes.
6. Remove from oven and let cool at least 5 minutes before serving.

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 MEAL PL AN

1
Recipes
211 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 SWEET ITALIAN SAUSAGE
PREP TIME COOK TIME SERVES

10 minutes + optional 15 - 20 minutes 10 - 20 servings

overnight chill time

2 teaspoons dried tarragon

¼ teaspoon dried oregano
¼ teaspoon dried rosemary
1 teaspoon sea salt
4 to 5 cloves garlic, crushed
¾ teaspoon minced fresh basil
3 tablespoons minced fresh parsley
3 pounds ground pork

1. Combine the dried spices in a spice grinder and grind to a fine powder. You can also grind the spices
with a mortar and pestle, clean coffee grinder, mini blender, or mini food processor.
2. Add the spices to the liquids, if called for, then add to the ground pork.
3. Mix to completely incorporate the spices into the meat. Cover with plastic wrap and refrigerate
overnight or up to 24 hours (optional).
4. Preheat the oven to 400°F.
5. orm 4- to 8-ounce patties with your hands and place on a rimmed cookie sheet, spacing about 1 inch
F
apart (how big you make these patties will depend on how big a serving size you are aiming for) just
as you would make hamburger patties. You may need two cookie sheets, depending on how thick you
make your patties.
6. ake the sausage patties for 15 to 25 minutes (depending on how thick they are) until the internal
B
temperature reaches a minimum of 160°F. Alternatively, you can fry sausage patties in a frying pan
or on a griddle over medium-high heat.
7. o freeze the sausage patties, place the patties on a cookie sheet to put in the freezer overnight and
T
then store them in a resealable freezer bag or container. You can reheat from frozen in the micro-
wave or by frying in a frying pan.

212 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 NEW ENGLAND CLAM
CHOWDER
PREP TIME COOK TIME SERVES

20 minutes 35 minutes 6 - 8 servings

4 thick slices bacon, chopped 1 green plantain, peeled and grated

1 onion, diced 2 bay leaves
2 to 3 stalks celery, thinly sliced 4 to 5 sprigs of thyme, leaves only
1 large carrot, diced 2 cups coconut cream
1 large turnip, cut into ¾-inch cubes 3 tablespoons chopped fresh parsley
3 cups any Bone Stock Sea salt or truffle salt, to taste
3 (5- to 6-ounce) cans clams, drained

1. lace the bacon in a medium stockpot, then turn on the heat to medium-high. Cook, stirring
P
occasionally, until the bacon is crisp.
2. dd the onion, celery, carrot, and turnip to the pot. Cook until fragrant, stirring occasionally,
A
about 5 minutes.
3. dd the stock, clams, plantain, bay leaves, and thyme. Bring to a boil, then reduce the heat to maintain
A
a simmer for 20 minutes. Stir occasionally.
4. dd the coconut cream and parsley. Taste and season with salt,
A
if desired. Cook for 1 to 2 minutes and serve.

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 MILD BARBACOA
PREP TIME COOK TIME SERVES

30 minutes + optional dry 2 ½ hours in a pressure 10 - 16 servings

rub overnight cooker, 10 ½ hours in a
slow cooker

5 to 7 pounds beef shoulder or brisket 1 medium-sized red onion, roughly cut

2 tablespoons dried oregano 1 head garlic, peeled and cloves smashed
1 tablespoon granulated garlic 5 bay leaves
1 tablespoon granulated onion 2 sticks cinnamon
1 tablespoon dried thyme (Mexican cinnamon, preferred)

1 tablespoon turmeric powder 3 tablespoons fish sauce

2 teaspoons ginger powder 1 tablespoon blackstrap molasses

1 tablespoon sea salt, divided Juice of 4 limes

1 medium bunch cilantro, roughly ½ cup apple cider vinegar

chopped 4 cups Beef Stock

1. Pat the beef shoulder dry with paper towels.

2. Combine the oregano, granulated garlic,
granulated onion, thyme, turmeric, ginger, and
1 teaspoon of salt in a bowl. Then rub the spices
all over the shoulder. If you’d like, you can wrap
seasoned shoulder in plastic wrap and refrigerate
overnight or up to 24 hours.
3. lace the cilantro, onion, and garlic in the bot-
P
tom of a pressure cooker or slow cooker. Wrap
the bay leaves and cinnamon sticks in butcher’s
twine to make a little bouquet garni and place in
the bottom of the pressure cooker or slow cooker
as well.
4. Place the seasoned beef shoulder on top of the
herbs.

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 5. dd the fish sauce, blackstrap molasses, lime juice, apple cider vinegar, and remaining salt. Pour the
A
beef stock into the pressure cooker or slow cooker until the beef shoulder is just covered. If you run
out of stock, top off with water.
6. ook the beef on high pressure for 2 hours in a pressure cooker, according to the manufacturer’s direc-
C
tions and following all safety protocols, or cook for 8 to 10 hours on low in a slow cooker.
7. Remove beef from pressure cooker or slow cooker, and let the beef cool 5 to 10 minutes.
8. Remove the bouquet garni, then simmer the cooking liquid uncovered until it is reduced by half. If
you’re using a slow cooker, transfer the liquid to a pot to simmer on the stovetop until reduced.
9. fter the beef has rested and while the liquid is simmering, shred the beef by using two forks and pull-
A
ing in opposite directions, repeatedly.
10. Once the liquid is reduced, place in a blender and blend on high for 30 seconds to form a smooth puree.
You should end up with about 5 cups of puree.
11. Pour the puree over the pulled beef and mix to evenly coat. Alternatively, you can pour only a few cups
first and then taste to see how you like it. Continue to add a little more puree until the beef is exactly
to your liking.
12. Serve in a lettuce wrap (or in Tortillas) with Guacamole and fresh limes!

215 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GUACAMOLE
PREP TIME COOK TIME SERVES

10 minutes - 3-4 servings

1½ large ripe avocados, or 2 smaller avocados

½ cup finely chopped fresh cilantro
1 tablespoon lime juice
½ teaspoon sea salt or truffle salt

1. Cut the avocados in half and scoop the flesh into a small bowl.
2. dd the remaining ingredients, mash with a fork to thoroughly mix, and serve. Store leftovers
A
in the fridge for up to a week.

216 THE AUTOIMMUNE PROTOCOL

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 PALEO FLOUR
TORTILLAS
PREP TIME COOK TIME SERVES

15 minutes 25 minutes 8 tortillas

1 ½ cups cassava flour

3
⁄4 teaspoon salt
¼ teaspoon cream of tartar
¹⁄8 teaspoon baking soda
3
⁄4 cups warm water
6 tablespoons extra virgin olive oil or avocado oil

1. Combine flour, salt, cream of tartar and baking soda in a mixing bowl. Add oil and water and
mix with a wooden spoon or your hands until a stiff dough forms. If dough is sticky, use a bit
more flour. If the dough is crumbly, add a bit more olive oil.
2. Divide dough in half, then in half again to create 8 fairly equal portions. Form each piece
into a ball.
3. Place one dough ball at a time on a silicone baker’s mat,
parchment paper or wax paper and flatten with the palm of
your hand as much as possible. Cover flattened dough with
a sheet of parchment paper or wax paper. Roll dough into
a very flat rough circle, about 8-10 inches in diameter.
Carefully remove the bottom silicone mat or parchment
paper, so the rolled-out tortilla is stuck to one piece of
parchment paper or wax paper. Set aside and roll out the
remaining dough balls (when they’re stuck to parchment
or wax paper, you can easily stack them in preparation for
cooking).
4. Preheat a 10” or larger skillet (a well-seasoned cast iron or
enameled cast iron pan works well) over medium heat (medi-
um-high heat if using a stainless steel pan).
5. When pan is hot, peel one rolled-out raw tortilla off its
parchment or wax paper and place into pan. Cook about 1
minute or until bottom surface has a few pale brown spots.

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 The top surface will begin to show a few little bubbles. Flip and cook for about 30-45 seconds.
[Ideally, the tortillas will be soft with a few small pale golden brown spots on surface. If tortilla is
browning too fast, reduced heat a bit. If it’s taking longer than a minute to see a few pale golden
brown spots on underside of tortillas, increase heat a bit.] Remove from pan with tongs and stack in
a covered container until all tortillas are cooked.
6. Serve warm or allow to cool for later use. Store in an airtight container or resealable plastic bag at at
room temperature for 24 hours or can be frozen indefinitely. To freeze, separate tortillas with
parchment paper or waxed paper and place in a zippered bag before placing in freezer.

218 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 LEMON-PARSLEY
CAULIFLOWER “RICE”
PREP TIME COOK TIME SERVES

15 minutes 7-9 minutes 3 - 6 servings

1 small head cauliflower (about 2 pounds)

3 to 4 tablespoons coconut oil or other cooking fat
1 clove garlic, crushed
1 tablespoon finely grated lemon zest (about 1 lemon)
1 tablespoon fresh lemon juice
¼ cup chopped fresh parsley
¹⁄8 teaspoon salt

1. ore the cauliflower and place the florets in a food processor (you may have to do this in
C
batches). Pulse until chopped to rice-grain size. Set aside. Alternatively, you can grate the
cauliflower with a box grater. Also, many stores sell fresh or frozen caulirice!
2. Heat 3 tablespoons of the oil in a large skillet or wok over medium-high heat.
3. dd cauliflower to the pan as well as salt and garlic. add remaining ingredients. Cook, stirring
A
frequently, until the cauliflower is cooked al dente (about 6 to 8 minutes, less if using frozen
store-bought caulirice). If the rice starts sticking to the pan or the pan looks very dry, add an
additional tablespoon of oil.
4. Stir in the remaining ingredients and cook 1 minute. Enjoy!

219 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SEASONED
SPATCHCOCK CHICKEN
PREP TIME COOK TIME SERVES

10 minutes 45 minutes 5-8 servings

+ 5-10 minutes rest time

4 cloves garlic, crushed

1 lemon, zested and juiced
2 tablespoons chopped fresh oregano
½ teaspoon chopped fresh thyme
½ teaspoon chopped fresh rosemary
1 teaspoon salt
2 tablespoons avocado oil, divided
4-6-pound whole chicken

1. Prepare the seasoning slurry. Mix crushed garlic, lemon zest, lemon juice, chopped oregano,
chopped thyme, chopped rosemary, salt and 1 tablespoon of avocado oil.
2. Rub 1 tablespoon of avocado oil over the bottom of a cast-iron or stainless steel skillet (10” or
bigger will fit most chickens).
3. Preheat oven to 425F.
4. Using poultry shears, cut along the right side of the chicken’s backbone (so you’re cutting
through the ribs and not the vertebrae) all
the way down the spine. Repeat down the
left side to entirely remove the backbone.
Turn chicken over (back to breast-side up)
and open up to begin to lie flat. You can more
thoroughly flatten the chicken by pulling up
on one side while pushing down on the other
(this breaks the ribs so the chicken will like
flat).
5. Place chicken skin-side-up inside prepared
skillet. Pat dry with paper towel. Rub sea-
soning slurry all over skin side of chicken.
6. Roast for 45 minutes. Let rest 5-10 minutes
in pan before serving.

220 THE AUTOIMMUNE PROTOCOL

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 ROASTED BROCCOLI
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

8 cups broccoli florets and cubed stems (about 2 pounds)

¼ cup avocado oil or olive oil
6 to 8 cloves garlic, minced
1 tablespoon finely grated lemon zest
¼ teaspoon sea salt or truffle salt
¼ cup chopped fresh parsley

1. Preheat the oven to 450°F.

2. I n a casserole dish, toss the broccoli (and cauliflower, if using) florets and stems with the avocado oil,
garlic, lemon zest, and salt.
3. oast for 25 to 35 minutes, until the broccoli and cauliflower are fully cooked (it depends on how big
R
the florets are and how soft you like them),
stirring once halfway through cooking.
4. Remove the dish from the oven, toss with the fresh parsley, and serve.

TIPS:
1. For a little extra zing, reserve the juice from the lemon and squeeze over the broccoli right before
serving.

221 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CELERY ROOT PUREE
PREP TIME COOK TIME SERVES

10 minutes 15 minutes 4-6 servings

¼ cup duck fat, unsalted butter, or ghee

2 large celery roots, peeled and chopped into ½-inch cubes
2 cups Bone Stock
Sea salt (optional)

1. Heat the duck fat over medium-high heat in a large skillet or saucepan. Add the celery root and sauté,
stirring frequently, until browned (8 to 9 minutes.)

2. Add ¼ cup of stock at a time, stirring frequently, adding the next quarter cup only when the stock has
almost completely evaporated. After adding the last addition of stock, immediately
remove from heat.
3. Puree using an immersion blender, countertop blender, or food processor. Taste and add salt,
if desired. Enjoy!

222 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SHRIMP SALAD
PREP TIME COOK TIME SERVES

20 - 30 minute none 2-3 servings

½ cup chopped fresh cilantro

3 tablespoons lime juice (about 2 limes)
3 tablespoons olive oil
2 tablespoons fish sauce
1 pound precooked shrimp
½ large fennel bulb, sliced extremely thin, about 3 cups
1 medium mango, peeled and diced
½ cup very finely sliced red onion
1 large avocado, diced

1. o make the dressing: combine the cilantro, lime juice, olive

T
oil, and fish sauce in a bowl or measuring cup. Set aside.
2. Toss the shrimp, fennel, mango, and onion in a bowl.
3. rizzle the dressing over the shrimp salad and toss to
D
completely coat.
4. dd the diced avocado and gently toss to incorporate. If
A
you’re making this salad ahead of time, keep the avocado
separate and add just before serving. Enjoy!

223 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GREMOLATA-TOPPED
FISH FILLETS
PREP TIME COOK TIME SERVES

15 minutes 20 minutes 4 servings

2 tablespoons olive oil, divided

¼ cup crumbled plantain chips
¼ cup chopped fresh parsley
1 clove garlic, crushed to a coarse paste
Finely grated zest and juice from 1 lemon
1 to 1½ pounds medium-firm fish fillets (such as seabass, mahi mahi, hali-
but, swordfish), cut into 4 pieces
¼ teaspoon sea salt

1. reheat the oven to 425°F. Line a rimmed baking sheet

P
with aluminum foil and spread the 2 tablespoons olive
oil over the top (alternately, use a silicone baking mat
and skip the olive oil).
2. ix the plantain chip crumbs with parsley, garlic,
M
lemon zest, and remaining one tablespoon olive oil.
3. lace the fish fillets on the prepared baking sheet.
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Drizzle with lemon juice and sprinkle with salt.
4. venly coat the top of the fish fillets with the crumb
E
mixture from Step 2.
5. ake for 15 to 20 minutes, until fish is fully cooked.
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Enjoy!

224 THE AUTOIMMUNE PROTOCOL

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 TOSTONES
PREP TIME COOK TIME SERVES

5 minutes 10 minutes (if frying in 4 servings

two batches)

2 green plantains
½ cup duck fat
salt, to taste

1. Peel green plantains by slicing just through the peel (not the fruit) lengthwise, from tip to tip,
then prying off the peel with your thumbs. Sometimes it’s easier to peel if you make more
than one slice down the length of the plantain.
2. Slice the peeled plantain at an angle into 1” thick slices.
3. Meanwhile, preheat a large stainless steel skillet on the stovetop over medium heat (skip this
step if using a gas stove).
4. Add a big dollop of duck fat to the hot skillet, then arrange the plantain slices in the skillet in
one layer (if your skillet is too small to fit all of them at once, cook in batches).
5. Fry the plantain for two to three minutes on each side until they are golden in color. I prefer to
flip three times as opposed to once to make sure they don’t get too brown. If they’re browning
too quickly, reduce the heat. Maintain at least an eighth of an inch of fat in the bottom of the
pan to prevent the plantain from sticking; add more fat as needed.
6. Remove the plantain slices from the skillet with tongs or a slotted spoon. Traditionally, they
are pounded flat with a hinged utensil made for the task, called a tostonera, or but any kitch-
en utensil (bowl, cup, plate etc.) that has a large enough flat surface will do the trick. I flatten
mine on a cutting board with my 4-cup measuring cup then peel the mashed plantain off the
bottom of the measuring cup with a spatula
directly into the hot skillet again. Be inventive:
there’s probably a dozen different things in your
kitchen that will flatten the fried plantain slices!
7. Fry the plantain slices a second time, this time
about one minute per side until crisp and golden
brown, adding additional duck fat as needed to
maintain about an eighth of an inch of fat in the
bottom of the pan. You’ll almost certainly have
to do this in two or even three batches, unless
you own the world’s biggest skillet.

225 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 8. Remove tostones from the skillet and place on a serving plate or cutting board lined with pa-
per towel to drain any excess fat. Sprinkle liberally with salt while still warm.
9. Tostones are best enjoyed right when you make them. Enjoy!

TIPS:
1. Peel green plantains by slicing just through the peel (not the fruit) lengthwise, from tip to tip,
then prying off the peel with your thumbs. Sometimes it’s easier to peel if you make more than
one slice down the length of the plantain.

226 THE AUTOIMMUNE PROTOCOL

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 SIMPLE FENNEL SALAD
PREP TIME COOK TIME SERVES

5-10 minutes none 3 - 4 servings

1 pound fennel (bulb, stems, and leaves)

Juice of 1 lemon (about 3 tablespoons)
1 tablespoon olive oil
¼ teaspoon sea salt

1. To make the dressing, mix the lemon juice, olive oil, and salt together in a small bowl. Set aside.
2. Thinly slice fennel bulb, and chop stems and leaves. A mandoline slicer makes this job very quick!
3. Gently toss the fennel with dressing and serve.

227 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BROILED PORK CHOPS
PREP TIME COOK TIME SERVES

10 minutes 15 minutes 4 servings

AIP HERBS DE PROVENCE

3 tablespoons dried marjoram leaves

3 tablespoons dried savory
3 tablespoons dried thyme leaves
1 teaspoon dried oregano leaves
1 teaspoon dried rosemary leaves
1 teaspoon dried tarragon
½ teaspoon dried rubbed sage

1. ombine the spices directly in a spice shaker or spice jar. (If you don’t have a spice shaker, you can
C
sprinkle the blends into food by hand or dust with a sieve).
2. Store in a pantry or cupboard for up to 6 months or freeze for up to 2 years.

BROILED PORK CHOP

1 to 2 tablespoons AIP Herbs de Provence

4 1- to 1 ½ -inch thick pork chops, about 8
ounces each (bone-in or boneless)

1. urn the broiler to high and let the oven preheat for about
T
10 minutes.
2. Sprinkle pork seasoning liberally over both sides of the pork chops.
3. lace the pork chops on a roasting pan, using the rack insert that
P
comes with the pan.
4. roil the pork chops on the first side for 6 to 8 minutes,
B
depending on the thickness of the chops. Flip and broil on
the second side for another 6 to 8 minutes.
5. Let the pork chops rest for 5 minutes before serving.

228 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BROILED ASPARAGUS
PREP TIME COOK TIME SERVES

5 minutes 6 - 8 minutes 2 - 4 servings

1 pound asparagus, tough ends of spears snapped off and discarded

2 tablespoons avocado oil
¼ teaspoon sea salt or truffle salt

1. osition a rack in the oven 6 inches below the broiler and preheat the broiler on high for 10 to
P
15 minutes.
2. lace the asparagus on prepared rimmed baking sheet. Drizzle with the oil and sprinkle with the salt;
P
toss to combine.
3. Broil for 6 to 8 minutes, until starting to brown. Enjoy!

229 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MAPLE AND SAGE ROASTED
WINTER SQUASH
PREP TIME COOK TIME SERVES

10 minutes 30 - 35 minutes 6 servings

2 pounds winter squash, peeled, seeded, and cut into 1½-inch pieces
3 tablespoons coconut oil, melted
2 tablespoons maple sugar
1 tablespoon chiffonade fresh sage
½ teaspoon sea salt

1. Preheat the oven to 425°F. Line a rimmed baking sheet with aluminum foil or parchment paper.
2. In a large bowl, toss the squash with the coconut oil, maple sugar, sage, and salt. Spread out onto the
prepared baking sheet.
3. Roast for 30 to 35 minutes, until slightly browned and tender.
4. Shake the pan (and toss the squash chunks) every 10 minutes during baking. Enjoy!

230 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MEAL PL AN

2
Recipes
231 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 BREAKFAST SAUSAGE
PREP TIME COOK TIME SERVES

10 minutes + optional 15 - 20 minutes 10 - 20 servings

overnight chill time

2 teaspoons sea salt

2 teaspoons rubbed sage
1 teaspoon ground mace
1 teaspoon dried thyme
¼ teaspoon ground ginger
½ teaspoon baking soda
¼ cup water
3 pounds ground pork

1. ombine the dried spices in a spice grinder and grind to a fine powder. You can also grind the spices
C
with a mortar and pestle, clean coffee grinder, mini blender, or mini food processor.
2. Add the spices to the liquids, if called for, then add to the ground pork.
3. ix to completely incorporate the spices into the meat. Cover with plastic wrap and refrigerate
M
overnight or up to 24 hours (optional).
4. Preheat the oven to 400°F.
5. orm 4- to 8-ounce patties with your hands and place on a rimmed cookie sheet, spacing about 1 inch
F
apart (how big you make these patties will depend on how big a serving size you are aiming for) just
as you would make hamburger patties. You may need two cookie sheets, depending on how thick you
make your patties.
6. ake the sausage patties for 15 to 25 minutes (depending on how thick they are) until the internal tem-
B
perature reaches a minimum of 160°F. Alternatively, you can fry sausage patties in a frying pan or on a
griddle over medium-high heat.
7. o freeze the sausage patties, place the patties on a cookie sheet to put in the freezer overnight and
T
then store them in a resealable freezer bag or container. You can reheat from frozen in the
microwave or by frying in a frying pan.

232 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 DIY BAKED CHICKEN
PREP TIME COOK TIME SERVES

5 minutes 30-40 minutes varies

Boneless, skinless chicken breast (see Tip)

Olive oil (about 1 tablespoon per chicken breast)
Seasoning Mix of choice (1 to 2 teaspoons per chicken breast)
Sea salt (if using seasoning mix without salt)

1. Preheat the oven to 350°F.

2. oat the chicken breast with the olive oil. Place on a rimmed baking sheet and sprinkle liberally with
C
the Seasoning Mix on both sides of the chicken. If using a mix that does not include salt, sprinkle a
little salt on each chicken breast as well, about ¹⁄8 to ¼ teaspoon per chicken breast.
3. ake 30 to 40 minutes, until the internal temperature reaches 165°F (the exact cooking time depends on
B
the thickness of the chicken, so adjust the time accordingly). Enjoy!

TIPS:
1. You can actually use any chicken pieces for this recipe, with or without the bone and skin,
including wings, legs, thighs or a mix of all of the above. However, you will need to adjust your
cooking time accordingly.

233 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ASPARAGUS SOUP
PREP TIME COOK TIME SERVES

10 minutes 25 minutes 5 - 6 servings

2 bunches asparagus (about 2½ pounds)

6 cups Chicken Stock, divided
1½ cups cubed green plantain (about 1 large plantain or 1½ medium)
2 cups cauliflower florets (about ½ small head)
Juice of 1 lemon
1 teaspoon sea salt
8 to 12 ounces lox, for garnish (optional)
1 cup plain coconut milk yogurt or kefir, for garnish (optional)

1. nap the tough stems off the asparagus. Add the tough stems to a large soup pot with 5 cups of the
S
stock, the plantain, and cauliflower. Bring to a boil and then reduce the heat to maintain a simmer.
2. immer for 15 to 20 minutes, until asparagus stems are soft when pierced with a knife and cauliflower
S
is overcooked. (For very tough stems, you may need to simmer longer.)

3. Meanwhile, slice the tender asparagus tips into ½-inch pieces.

4. In a blender in two batches or with an immersion blender, puree the contents of the pot until a
completely smooth puree forms (this takes 1 to 2 minutes in a blender, but may take longer with an
immersion blender).
5. ring the remaining 1 cup of stock and sliced asparagus tips to a simmer on the stovetop (do this in a
B
separate small pot if you opted to puree using an immersion blender, or in the same pot if you opted to
use your countertop blender). Simmer for 3 to 5 minutes until tender but not too soft.
6. dd the tender asparagus tips and stock to puree
A
in your soup pot. Stir in lemon juice and salt.
7. Stir and taste to see if it’s seasoned to your liking.

234 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MEATLOAF
PREP TIME COOK TIME SERVES

20 minutes, + 1 hour, 40 minutes 5-8 servings

marinating

2 to 3 tablespoons tallow, olive oil, or 1 tablespoon chopped fresh chives

avocado oil 1 pound frozen liver
1 medium-sized yellow onion, minced 1 pound ground pork
2 stalks celery, minced 1 pound ground beef
1 medium carrot, minced 1 tablespoon blackstrap molasses
4 cloves garlic, minced 2 tablespoons coconut aminos
¼ cup chopped fresh parsley 3 tablespoons apple cider vinegar
3 tablespoons chopped fresh basil 1 tablespoon fish sauce
3 tablespoons chopped fresh oregano
1 tablespoon chopped fresh thyme

1. Heat the tallow in a frying pan over medium-high heat. Add the onion, celery, and carrot and sauté
until soft and starting to brown, about 8 to 10 minutes. Set aside to cool before adding to the meat
mixture in Step 3.
2. Grate frozen liver with a box grater.
3. ombine all the ingredients in a large bowl. Mix together very
C
thoroughly. Cover and refrigerate for 4 to 6 hours or up to over-
night to let the flavors “marinate” or combine.
4. Preheat the oven to 350°F.
5. ress the meat mixture into a 9” x 5” loaf pan. Place the loaf pan
P
on a cookie sheet or in a larger baking pan before placing in the
oven.
6. ake for 1 hour and 40 minutes, or until internal temperature
B
reaches 160°F.
7. Let the meatloaf sit for 5 to 10 minutes before serving.

235 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MASHED PLANTAIN
PREP TIME COOK TIME SERVES

10 minutes 15 minutes 6 - 8 servings

3 green plantains (also called raw bananas)—the greener, the better!

6 oz bacon
1 medium yellow onion
4 cloves garlic
(extra bacon grease, lard, or butter may be used to make a
thinner mash)

1. Peel plantains and cut into 1” semi-circles. I made that sound too easy. Peeling green plantains can be
an exercise in frustration. Cut in half lengthwise and then in half crosswise. Get your thumbs under
the peel and pry off. If the peel breaks, use a paring knife to cut off whatever is stuck on.
2. Place plantains into a pot with 2” of water. Bring to a boil over high heat and then reduce to maintain a
simmer. Simmer covered until plantains are tender when pierced with a knife, about 20 minutes.
3. Meanwhile, cut bacon into small pieces (I like a pair of scissors for this job). Dice onion finely and finely
chop garlic.
4. Add bacon to a cold frying pan then turn on the heat to medium high. Cook bacon 5 minutes, then add
onion and garlic, stirring occasionally. Continue cooking until bacon is crisp and onion is soft and
vcaramelized.
5. Drain plantains when they are finished cooking, but keep the
cooking liquid! (I like to drain into a large pyrex measuring cup).

6. Add ½ cup cooking liquid back to the plantains. Mash with a wire
potato masher to your desired
consistency. Add bacon, onion, garlic and all of the grease from
the pan. Stir to incorporate.
7. If you like a thinner mash, you can either add more of the cooking
liquid or you can add additional bacon grease (or substitute lard
or butter). Mofongo tends to get thicker as it sits, so if you have
any leftovers, you will likely want to add some liquid to them
before reheating. Enjoy!

236 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SHAVED BRUSSELS SLAW
WITH APPLE & MINT
PREP TIME COOK TIME SERVES

10-20 minutes 10 minutes 5-8 servings

4 ounces pancetta, diced (bacon works as a substitute)

2 pounds Brussels sprouts (see Tips)
1 clove garlic, minced
1 lemon (2 tablespoons lemon juice and 1 teaspoon
finely grated lemon zest)
2 tablespoons olive oil
½ teaspoon sea salt
1 Granny Smith apple, cored and thinly sliced
¹⁄3 cup mint chiffonade (see Tips)

1. lace the diced pancetta in a cold skillet and turn on the heat to medium. Sauté, stirring occasionally,
P
until browned, about 8 minutes. Remove the pancetta from the skillet and set aside to cool while you
prepare the rest of the ingredients.
2. lice the Brussels sprouts very thinly, discarding the stem or an
S
easier method is to trim of the stem first and use a mandoline
slicer or a food processor with a slicer attachment. Two pounds of
whole Brussels sprouts will give you about 12 ounces shaved.
3. ombine all the ingredients in a bowl and thoroughly mix to serve
C
immediately. Leftover slaw can be stored in the fridge for up to 5
days. Enjoy!

TIPS:
1. To chiffonade mint, stack several mint leaves on top of each
other and slice very thin strips across the leaves all the way
down. Measure ¹⁄3 cup after you chiffonade the mint; it will be
close to 1 cup of loosely packed leaves before you chiffonade.
2. To save yourself time, feel free to purchase 1 (10- to 12-ounce)
bag of shaved Brussels sprouts instead of 2 pounds of whole
Brussels sprouts.

237 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 HAMBURGER STEW
PREP TIME COOK TIME SERVES

15 minutes 50 minutes 5 - 6 servings

3 tablespoons olive oil, divided 5 sprigs thyme

2 medium zucchini, peeled and roughly 2 pounds ground beef
chopped 2 teaspoons sea salt
3 cups Bone Stock 8 ounces mushrooms, sliced
1 medium white onion, roughly chopped 2 green plantains, peeled and chopped
3 medium carrots, sliced into ½-inch into ½-inch cubes
rounds Chopped fresh parsley, for garnish
3 stalks celery, sliced into ½-inch slices (optional)
1 bay leaf
1 sprig rosemary

1. eat 2 tablespoons of the olive oil in a large stockpot or Dutch oven over medium-high heat. Add the
H
chopped zucchini and sauté, stirring frequently, until zucchini is browned and soft, about 8 to 10
minutes.
2. Remove the zucchini from the pot and place in a blender and the pour in the stock. Blend on high until
completely smooth, 1 to 2 minutes. Set aside.
3. dd the remaining tablespoon of olive oil to the pot. Add the
A
onion, carrots, and celery and sauté, stirring frequently, until
onion is starting to caramelize, about 7 to 8 minutes. Add the
bay leaf, rosemary, and thyme.
4. dd the ground beef to the vegetables, break up into large chunks
A
with a spoon or spatula, and season with the salt. Brown, stirring
infrequently to avoid breaking the meat up into too small of
pieces, for 8 to 10 minutes.
5. dd the mushrooms, plantain, and zucchini puree to the pot. Bring
A
to a simmer, and then reduce heat to medium-low and cook
uncovered for 20 minutes, stirring occasionally. Taste for
seasoning and add more salt if desired.
6. emove the thyme and rosemary stems as well as the bay leaf
R
before serving. Garnish with parsley, if desired.

238 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BROILED SALMON
PREP TIME COOK TIME SERVES

15 minutes 10 minutes 4 servings

4 (6- to 8-ounce) salmon fillets

½ teaspoon truffle salt or sea salt
1½ teaspoons fresh thyme leaves (from 5 to 6 sprigs)

1. lace a rack high up in the oven so that the surface of the salmon will be 6 to 8 inches away from the
P
top element. Turn the broiler on high (let it preheat about 10 minutes before putting the salmon in the
oven). Coat a rimmed baking sheet with olive oil.
2. Place the salmon fillets skin side down on the oiled baking sheet.
3. Sprinkle with truffle salt and fresh thyme.
4. roil for 8 to 9 minutes, until fully cooked (when segments flake apart easily and salmon is opaque
B
throughout). Enjoy!

239 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 LEMON-PARSLEY
CAULIFLOWER “RICE”
PREP TIME COOK TIME SERVES

15 minutes 7-9 minutes 3 - 6 servings

1 small head cauliflower (about 2 pounds)

3 to 4 tablespoons coconut oil or other cooking fat
1 clove garlic, crushed
1 tablespoon finely grated lemon zest (about 1 lemon)
1 tablespoon fresh lemon juice
¼ cup chopped fresh parsley
¹⁄8 teaspoon salt

1. ore the cauliflower and place the florets in a food processor (you may have to do this in
C
batches). Pulse until chopped to rice-grain size. Set aside. Alternatively, you can grate the
cauliflower with a box grater. Also, many stores sell fresh or frozen caulirice!
2. Heat 3 tablespoons of the oil in a large skillet or wok over medium-high heat.
3. dd cauliflower to the pan as well as salt and garlic. add remaining ingredients. Cook, stirring
A
frequently, until the cauliflower is cooked al dente (about 6 to 8 minutes, less if using frozen
store-bought caulirice). If the rice starts sticking to the pan or the pan looks very dry, add an
additional tablespoon of oil.
4. Stir in the remaining ingredients and cook 1 minute. Enjoy!

240 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SIMPLE FENNEL SALAD
PREP TIME COOK TIME SERVES

5-10 minutes none 3 - 4 servings

1 pound fennel (bulb, stems, and leaves)

Juice of 1 lemon (about 3 tablespoons)
1 tablespoon olive oil
¼ teaspoon sea salt

1. To make the dressing, mix the lemon juice, olive oil, and salt together in a small bowl. Set aside.
2. Thinly slice fennel bulb, and chop stems and leaves. A mandoline slicer makes this job very quick!
3. Gently toss the fennel with dressing and serve.

241 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SHRIMP PAD THAI
PREP TIME COOK TIME SERVES

10 minutes 10 minutes 2-4 servings

2 tablespoons coconut oil

4 cloves garlic, minced
3 tablespoons fish sauce
1 tablespoon coconut aminos (or use 1 more tablespoon fish sauce)
¼ cup lime juice (about 2 limes)
1½ teaspoons coconut water vinegar
1 (12-ounce) bag broccoli slaw
2 medium carrots, cut into thin julienne strips
16 to 20 ounces salad shrimp, precooked and tails off
4 to 5 green onions, finely chopped
5 tablespoons chopped fresh cilantro

1. eat a large frying pan or wok over medium-high

H
heat. Add the coconut oil and garlic. Cook 1 min-
ute, until garlic is starting to brown and become
fragrant.
2. dd the fish sauce, coconut aminos, lime juice,
A
coconut water vinegar, garlic, broccoli slaw, and
carrots. Cook, stirring frequently, until broccoli
slaw and carrots are cooked al dente, about 5 to 7
minutes.
3. dd the shrimp and cook an additional 1 to 2
A
minutes, stirring frequently, just until shrimp are
warmed.
4. dd the green onions and cilantro, and cook for
A
30 more seconds. Remove from heat and serve.

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by Dr. Sarah Ballantyne, PhD
 MEAL PL AN

3
Recipes
243 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 BEEF HEART SAUSAGE
PREP TIME COOK TIME SERVES

10 minutes 20 minutes 8 - 20 servings

½ teaspoon dried thyme leaves

½ teaspoon dried savory
2½ teaspoons salt
3 pounds ground beef heart
1 pound ground pork
1 pound ground pork fat or additional ground pork
½ cup dry red wine

1. Combine the dried spices in a spice grinder and grind until they are a fine powder. You can also
do this in a mortar and pestle, clean coffee grinder, mini blender, or mini food processor.
2. Place the dried herbs, salt, ground meat, and any other ingredients in a large mixing bowl.
3. Use your hands to thoroughly incorporate the spices into the meat. Alternatively, mix the
ingredients in the bowl of a stand mixer on low speed for 3 to 4 minutes.
4. Cover with plastic wrap and refrigerate overnight or up to
24 hours.

TO STUFF INTO CASINGS:

5. Follow the directions on the packaging for your natural hog
casings (typically rinsing and then soaking them in warm
water for 30 minutes).
6. Attach the sausage stuffer attachment to the meat grinder
per the manufacturer’s instructions. Alternatively, you can
use a manual sausage stuffer (a contraption that is vaguely
reminiscent of a water pump) or even a jerky gun or pastry
bag without a tip attached.
7. Grease the funnel end of your sausage stuffer attachment
with lard, palm shortening, or coconut oil. Feed the sausage
casing onto the funnel until the entire casing is scrunched/
folded up on the funnel, leaving only 3 to 4 inches over the
end (to tie a knot when you’re done—but leave it untied for
now so you don’t get air bubbles in your sausage).

244 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 8. Turn on your meat grinder per the manufacturer’s instructions (typically on low speed for stuffing
sausages). Feed your sausage mix through the feeding spout, pressing down with the tamping tool or
a wooden pestle. If you are using a manual sausage stuffer, fill the feeding tube with the sausage mix
and then press down on the handle to push the sausage mix into the casing.
9. As the sausage mix fills the casing, it will gradually inflate, ease away from the funnel, and coil in
ropelike fashion. Make sure that the casing is filling completely, but do not overstuff your sausage,
or the casing may burst when you cook it. If you want kinks in your sausage to make links, simply
pause and twist a few times to create a kink.
10. Fill the casing to within 3 to 4 inches of the other end. Tie a knot in both ends and set aside.
11. Repeat until all of your sausage mix has been stuffed into casings.
12. To parboil your sausage, attach an oil/candy thermometer to the side of a large stockpot.
13. Fill the pot half to three-quarters full with water (you can add a teaspoon of saltto make it heat fast-
er). Bring the water up to 165°F, just shy of a simmer. Place the sausages in the pot (do not overfill;
you may have to do this in batches depending on how big your pot is). Keep the temperature as close
to 165°F as you can.
14. Poach the sausages until the internal temperature reaches 150°F (15 to 20 minutes, depending on the
size of the sausages).
15. Remove from the pot and set aside. If freezing, refrigerate the sausage until cold and then slice into
single servings before freezing. Freeze on a baking sheet, then move to a resealable freezer bag or
container.
16. Fry in a skillet over medium heat for 5 to 10 minutes (longer if
frying frozen) and enjoy! You can also freeze after pan-frying if
you want to be able to reheat your sausages from frozen in the
microwave for a very quick breakfast.

TO FORM INTO PATTIES:

17. Preheat the oven to 400°F.
18. Form 4- to 8-ounce patties with your hands, just as you would
make hamburger patties. Place on a rimmed baking sheet, spac-
ing them about 1 inch apart (how big you make the patties will
depend on how big a serving size you are aiming for). You may
need 2 baking sheets, depending on how thick you make your
patties.
19. Bake for 15 to 25 minutes (depending on thickness), until the in-
ternal temperature reaches a minimum of 160°F for beef, lamb,
and pork sausage and 165°F for chicken and turkey sausage.
Alternatively, you can fry the patties in a skillet or on a griddle
over mediumhigh heat.
20. If freezing, freeze on a baking sheet, then move to a resealable
freezer bag or container. You can reheat frozen patties in the
microwave or fry them in a skillet.

245 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 APPLESAUCE
PREP TIME COOK TIME YIELD

10-30 minutes 20 minutes 3 cups

4 or 5 apples (about 2½ pounds)

¼ cup water

1. Peel and core the apples. There’s no need to cut them up too small.
2. Place the apples and water in a large pot and cover. Bring to a simmer over high heat, then reduce the
heat to medium.
3. Simmer until the apples are soft, about 20 minutes (less if your apple pieces are smaller, more if they
are larger). The cooking time will also vary depending on the apple variety.
4. Let cool. Mash with a potato masher or fork for a lumpier consistency or with an immersion blender
for a smoother consistency. Some varieties of apple won’t need to be mashed at all. Enjoy!

246 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 VEGETABLE SOUP WITH
CHICKEN SAUSAGE
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

4 cups Bone Stock 1½ cups chopped carrot greens

1 cup sliced leeks ¼ to ½ recipe Apple Chicken Sausage
1½ cups sliced carrots (optional, recipe on next page)

½ cup diced turnip ¼ teaspoon salt, plus more to taste

½ cup diced kohlrabi

1. Position an oven rack so that your lamb chops will be about 6 inches from the top element in your
oven. Preheat the broiler on high for 10 minutes while you prepare the lamb.
2. Combine the crushed garlic, grated lemon zest, oregano, and salt.
3. Pat the lamb chops dry with paper towels and place on a roasting pan. Rub the seasoning mix all over
the top and bottom of the chops.
4. Broil for 4 to 8 minutes per side (depending on the thickness of your lamb chops), until the internal
temperature reaches 145°F for medium-rare or 160°F for medium.
5. Let the chops rest for 5 minutes. Enjoy!

247 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 APPLE CHICKEN SAUSAGE
PREP TIME COOK TIME SERVES

20-40 minutes for patties, 8-16 minutes 4-6 servings

1-2 hours if stuffing into
casings + 24 hours
marinating time

1 medium onion, very finely ½ teaspoon dried marjoram leaves

chopped 1½ teaspoons salt
1 to 2 tablespoons cooking fat 4 pounds ground chicken or turkey
2 large Granny Smith apples, (or substitute pork)
peeled and diced ¼ cup minced fresh parsley
2 teaspoons dried rubbed sage
1 teaspoon dried thyme leaves
½ teaspoon dried rosemary

1. Turn on your meat grinder per the manufacturer’s instructions (typically on low speed for stuffing
sausages). Feed your sausage mix through the feeding spout, pressing down with the tamping tool or
a wooden pestle. If you are using a manual sausage stuffer, fill the feeding tube with the sausage mix
and then press down on the handle to push the sausage mix into the casing.
2. As the sausage mix fills the casing, it will gradually inflate, ease away from the funnel, and coil in
ropelike fashion. Make sure that the casing is filling completely, but do not overstuff your sausage,
or the casing may burst when you cook it. If you want kinks in your sausage to make links, simply
pause and twist a few times to create a kink.
3. Fill the casing to within 3 to 4 inches of the other end. Tie a knot in both ends and set aside.
4. Repeat until all of your sausage mix has been stuffed into casings.
5. To parboil your sausage, attach an oil/candy thermometer to the side of a large stockpot.
6. Fill the pot half to three-quarters full with water (you can add a teaspoon of saltto make it heat
faster). Bring the water up to 165°F, just shy of a simmer. Place the sausages in the pot (do not
overfill; you may have to do this in batches depending on how big your pot is). Keep the temperature
as close to 165°F as you can.
7. Poach the sausages until the internal temperature reaches 150°F (15 to 20 minutes, depending on
the size of the sausages).
8. Remove from the pot and set aside. If freezing, refrigerate the sausage until cold and then slice into
single servings before freezing. Freeze on a baking sheet, then move to a resealable freezer bag or
container.

248 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 9. Fry in a skillet over medium heat for 5 to 10 minutes (longer if frying frozen) and enjoy! You can also
freeze after pan-frying if you want to be able to reheat your sausages from frozen in the microwave
for a very quick breakfast.

TO FORM INTO PATTIES:

10. Preheat the oven to 400°F.
11. Form 4- to 8-ounce patties with your hands, just as you would make hamburger patties. Place on a
rimmed baking sheet, spacing them about 1 inch apart (how big you make the patties will depend on
how big a serving size you are aiming for). You may need 2 baking sheets, depending on how thick
you make your patties.
12. Bake for 15 to 25 minutes (depending on thickness), until the internal temperature reaches a mini-
mum of 160°F for beef, lamb, and pork sausage and 165°F for chicken and turkey sausage. Alternative-
ly, you can fry the patties in a skillet or on a griddle over mediumhigh heat.
13. If freezing, freeze on a baking sheet, then move to a resealable freezer bag or container. You can
reheat frozen patties in the microwave or fry them in a skillet.

249 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GREEK-INSPIRED
LAMB CHOPS
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

3 cloves garlic, crushed

1 tablespoons finely grated lemon zest (about 1 lemon)
1 tablespoons minced fresh oregano
¼ teaspoon salt
2 pounds lamb chops (rib or loin)

1. Position an oven rack so that your lamb chops will be about 6 inches from the top element in your
oven. Preheat the broiler on high for 10 minutes while you prepare the lamb.
2. Combine the crushed garlic, grated lemon zest, oregano, and salt.
3. Pat the lamb chops dry with paper towels and place on a roasting pan. Rub the seasoning mix all over
the top and bottom of the chops.
4. Broil for 4 to 8 minutes per side (depending on the thickness of your lamb chops), until the internal
temperature reaches 145°F for medium-rare or 160°F for medium.
5. Let the chops rest for 5 minutes. Enjoy!

250 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MASHED ACORN SQUASH
WITH FORTY CLOVES
OF GARLIC
PREP TIME COOK TIME SERVES

20 - 30 minutes 1 hour 15 minutes - 6-8 servings

1 hour 30 minutes

2 large acorn squash

(1½ pounds each)
3 to 4 heads garlic, peeled
1½ teaspoons avocado or coconut oil
1 teaspoon truffle salt
2 tablespoons extra-virgin

1. Preheat the oven to 350°F.

2. Cut the acorn squash in half and remove the seeds. Place the halves cut side up on a rimmed baking
sheet.
3. In a bowl, toss the garlic cloves with the avocado oil and distribute evenly among the 4 squash half
middles.
Sprinkle the squash halves with the truffle salt.
4. Roast for 1 hour 15 minutes to 1 hour 30 minutes, until the squash is soft.
5. Scoop out the squash and garlic and mash with a fork. Mix in the olive oil and serve.

251 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CAULIFLOWER “RICE”
PREP TIME COOK TIME SERVES

15 minutes 7-9 minutes 3 - 6 servings

1 small head cauliflower (about 2 pounds)

3 to 4 tablespoons avocado oil or other cooking fat
¹⁄8 teaspoon salt

1. Core the cauliflower and place the florets in a food processor (you may have to do this in
batches). Pulse until chopped to rice-grain size. Alternatively, you can grate the cauliflower
with a box grater. Set aside.
2. Heat 3 tablespoons of the oil in a large skillet or wok over medium-high heat.
3. Add the cauliflower to the pan and cook, stirring frequently, until the cauliflower is cooked
al dente, 6 to 8 minutes. If the rice starts sticking to the pan or the pan looks very dry, add an
additional tablespoon of coconut oil.
4. Stir in salt and cook for 1 minute. Enjoy!

252 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ROASTED CHICKEN
PREP TIME COOK TIME SERVES

10-15 minutes 1 -2 hours (depending 10-18 servings

on size of chicken)

2 (4- to 6-pound) whole chickens

3 to 4 tablespoons Poultry Seasoning
1 tablespoon pink or gray
salt or truffle salt

1. Preheat the oven to 350°F.

2. Place the chickens breast side up on a roasting pan. Remove the giblets and neck, if included
Sprinkle the entire surface of each chicken liberally with the seasoning mix and salt. Place an
ovensafe meat thermometer into the breast or thigh of the larger chicken.
3. Bake for 20 minutes per pound (for your bigger chicken) or until the internal temperature
reaches at least 165°F.
4. Let rest for 5 to 10 minutes before carving. Enjoy!

253 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 WHOLE CARROT
“TABOULEH”
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

3 to 4 large carrots, with greens attached (about 1½ pounds)

1½ teaspoons minced fresh mint
2 tablespoons raisins
2 tablespoons extra-virgin olive oil
2 tablespoons fresh lemon juice
½ teaspoon finely grated lemon zest
Pinch of salt

1. Cut the greens off the carrots. Remove the main stems (unless they are very tender) and finely chop
the leaves. Cut the carrots into large chunks.
2. Place the carrots in a food processor fitted with an S-shaped blade. Process until couscous-sized, 30
seconds
to 1 minute.
3. Toss the processed carrots with the chopped carrot leaves, mint,
raisins, olive oil, lemon juice and zest, and salt. Serve!

TIPS:
1. You can make this salad up to 24 hours ahead and just give it a
quick stir before serving. In fact, it tastes even better the next
day. Can’t find carrots with the greens attached? Use parsley
instead of carrot greens. Enjoy!

254 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MINT PESTO
ZUCCHINI “PASTA”
PREP TIME COOK TIME SERVES

15 minutes, +1 hour 15 - 18 minutes 2-4 servings

to salt zucchini

2 pounds zucchini (about 3 medium)

1 tablespoon salt
8 to 10 cloves garlic, unpeeled
2 tablespoons extra-virgin olive oil
2 tablespoons chopped fresh mint
2 to 3 tablespoons lard, coconut oil, or bacon fat

1. Slice the zucchini into long, thin noodles with a spiral vegetable slicer, mandoline slicer, or julienne
peeler. (With some patience, you can also julienne long strips of zucchini with a knife.) Sprinkle
liberally with the salt and place in a colander in the sink for 1 hour (this helps remove excess water
so that the zucchini holds together better once cooked).
2. Meanwhile, make the mint pesto: Place the whole, unpeeled garlic cloves in a dry pan. Heat over
medium-high heat, stirring or shaking the pan occasionally, until the papery peel of the garlic browns
and starts to flake off, about 10 minutes.
3. Remove the garlic from the pan and let cool enough to handle.
Remove the peel. Place the garlic, olive oil, and mint in a mini food
processor and pulse until you get a pastelike texture, or grind the
ingredients to a paste by hand using a mortar and pestle.
4. Rinse the zucchini noodles thoroughly. Drain and invert onto paper
towels or a clean kitchen towel. Place another kitchen towel or
paper towels on top and gently press to remove as much water as
possible.
5. Heat the lard in a large skillet or wok over medium-high heat. Add
the zucchini noodles once the pan is hot. Cook, stirring gently but
frequently, until the zucchini is cooked al dente, 5 to 8 minutes.
Keep the heat high enough that any liquid released by the zucchini
is evaporating. If you a lot of liquid accumulates in the bottom of the
pan, turn up the heat.
6. Remove from the heat and toss with the mint pesto. Serve.

255 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ROASTED RADISHES
PREP TIME COOK TIME SERVES

5-10 minutes 20-25 minutes 3-4 servings

1 pound radishes (about 3 bunches), trimmed and quartered

3 tablespoons lard, tallow, or duck fat, melted
¾ teaspoon salt

1. Preheat the oven to 375°F. Line a rimmed baking sheet with aluminum foil or a silicone liner for
easier cleanup.
2. In a small bowl, toss the radishes with the melted fat.
3. Spread on the prepared baking sheet and sprinkle with the salt.
4. Roast for 20 to 25 minutes, until the radishes start to turn golden brown. Enjoy!

256 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CINNAMON BROILED
GRAPEFRUIT
PREP TIME COOK TIME SERVES

5-10 minutes 4 to 6 minutes 2 servings

1 grapefruit
¼ teaspoon ground cinnamon

1. Position a rack in your oven so that the grapefruit will be about 6 inches from the top element.
Preheat the broiler on high for 10 minutes while you prepare the grapefruit.
2. Cut the grapefruit in half. Use a grapefruit knife or paring knife to cut around each segment. Place
the grapefruit halves cut side up on a roasting pan.
3. Sprinkle the top of the grapefruit with the cinnamon.
4. Broil for 5 to 6 minutes, until the grapefruit starts to bubble and brown on the top.

257 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 STEAMED CLAMS
PREP TIME COOK TIME SERVES

10 minutes 8-12 minutes 2-6 servings

4 to 5 pounds littleneck clams

3 tablespoons lard, bacon fat, or coconut oil
5 cloves garlic, minced
1 tablespoon finely grated
lemon zest (about 1 lemon)
½ cup white wine or a combination of 6 tablespoons Bone Stock
and 2 tablespoons fresh lemon juice
3 tablespoons chopped
fresh parsley
1 lemon, halved

1. Rinse the clams under cool water. Discard any that do not close when gently tapped.
2. Heat the lard, garlic, and lemon zest in a large pot (one that has a tight-fitting lid, ideally glass) over
medium-high heat. Cook for 3 to 4 minutes, until fragrant.
3. Place the clams in the pot. Add the wine, cover, and cook until the clams open, 5 to 8 minutes. Stir and
check frequently to remove individual clams as they open, adding a little water if necessary.
4. Remove the clams from the pot.
Remove and discard any clams that did not open. Sprinkle with parsley and drizzle with fresh lemon
juice. Enjoy!

TIPS:
1. You can use any type of clam for this
recipe. Depending on how big they are, you may
need to adjust the cooking time.

258 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BACON-BRAISED
WHITEFISH AND BRUSSELS
PREP TIME COOK TIME SERVES

15 minutes 50 minutes 3-6 servings

8 ounces bacon, cut into small pieces

1 pound Brussels sprouts, halved if large
1 small bunch kale, chopped (about 5 cups)
1½ to 2 pounds whitefish fillets, such as cod, hake, tilapia, or halibut,
cut into 2-inch-wide pieces
3 cloves garlic, crushed
1 teaspoon finely grated lemon zest
Juice of 1 lemon
1 cup Bone Stock

1. Place the bacon in a big saucepot or extra-large skillet, then turn on the heat to medium-high. Cook the
bacon until it is crisp, stirring occasionally, about 10 minutes. If the bacon is very fatty, drain off a little
fat, leaving 2 to 3 tablespoons of fat in the pan.
2. Add the Brussels sprouts and 2 to 3 tablespoons of the broth to the
pan. Cook, stirring frequently, until the Brussels sprouts are fully
cooked, about 20 minutes. When the broth evaporates, add another
2 to 3 tablespoons to the pan (this will likely happen 3 to 5 times).
Try to maintain ¹⁄6 to ¹⁄8 inch of liquid in the pan. If you run out of
broth before the Brussels sprouts are fully cooked, just use water.
3. Once the Brussels sprouts are done, add the kale (and a little more
broth or water if needed). Once the kale starts to wilt (3 to 4 min-
utes), move the vegetables to the side of the pan and
add the fish to the middle (again, add 1 to 2 tablespoons of broth or
water, if needed).
4. Stir the fish gently and minimally. Once cooked (4 to 10 minutes,
depending on how thick the pieces are), add the crushed garlic,
lemon zest, and lemon juice and cook for 1 to 2 more minutes. Enjoy!

259 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GARDEN GREEN VICHYSSOISE
PREP TIME COOK TIME SERVES

20 minutes 30 to 35 minutes, 6-8 servings

+ 4 hours chilling time

4 cups Bone Stock

1 head cauliflower, cored and cut into florets 3 leeks (green and white
parts), chopped
2 cups packed fresh spinach (about 4 ounces)
½ teaspoon salt, plus more to taste
¼ cup lard, avocado oil, or olive oil
3 to 4 avocados, peeled, pitted, and finely chopped, for serving
6 to 8 tablespoons chopped fresh cilantro, for serving
6 to 8 tablespoons Coconut Milk Yogurt, for serving (optional)

1. Combine the broth, cauliflower, and leeks in a large pot. Cover and bring to a boil over high heat,
then reduce the heat to maintain a simmer. Simmer for 25 to 30 minutes, until the vegetables are soft.
2. Add the spinach and simmer for 3 to 4 minutes, until the spinach has wilted. Remove from
the heat and let cool.
3. Add the lard. Purée the soup with an immersion blender, or pour into a blender and process until
smooth. Season with salt to taste.
4. Refrigerate the soup until cold, about 4 hours.
5. To serve, add half a chopped avocado and 1 tablespoon fresh cilantro to each bowl. Serve with a dollop
of Coconut Milk Yogurt, if desired. Enjoy!

260 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SWEET POTATO CHIPS
PREP TIME COOK TIME SERVES

15 minutes 45 minutes 10- 12 servings

6 long skinny sweet potatoes (about 1½” thick at the most)

1 tablespoon Salt
4-6 cups palm shortening (enough to have 1½”-2” of oil in your pot)

1. Slice sweet potatoes as thinly as possible (I sliced mine ¹⁄8” thick on my mandolin slicer and left the peel
on. You can peel them first if you prefer.)
2. Generously sprinkle sweet potato slices with salt, place in a colander in your kitchen sink and let drain
for 1-2 hours (or more).
3. Rinse excess salt off sweet potato slices and pat dry with clean tea towels or paper towel. It’s really
important that these slices are dry before they are put into the oil. Any excess water on them will
cause the oil to bubble aggressively.
4. Meanwhile, heat palm shortening in a fairly deep, wide bottomed pot with an oil thermometer at-
tached to the side. Aim to get the oil to 375F (or slightly hotter since it will cool down when you add
the sweet potato). You need to try and figure out exactly what setting to have your element on to keep
the oil at that temperature. For my stove, it was a touch over the 8.
5. Add a generous handful of sweet potato slices to the oil by gently slipping then into the oil with your
hand quite close to the surface. Use your strainer or skimmer to push the slices apart. Make sure the
oil comes back to temperature quite quickly. Watch them. When they stop bubbling a lot, start to curl
slightly, and brown a bit, they are done. It takes about 2 minutes if your oil comes back to temperature
quickly. It takes a bit longer if there is a lag time in getting your
oil back up to 375F.
6. Use your strainer or skimmer to scoop the sweet potato chips
out of the oil and place on your prepared paper towels to cool. I
found that mine had enough residual salt that they didn’t need
any more. Taste yours and see if they are salty enough. If not,
sprinkle some salt over the top while they are still warm.
7. Repeat in batches, each time making sure your oil comes back up
to 375 F.
8. Let the chips cool to room temperature and enjoy!

261 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 “SPAGHETTI”
PREP TIME COOK TIME SERVES

15 minutes 30 - 1 ½ hours 4-5 servings

3 to 4 pounds spaghetti squash 1 cup sliced black olives

(2 small or 1 large) (1 [4-ounce] can)
1 pound ground beef ¼ cup chopped fresh basil
1 pound ground lamb ¼ cup chopped fresh oregano
1 medium onion 2 tablespoons kuzu starch or arrowroot
10 to 12 cloves garlic, sliced powder
½ pound mushrooms, sliced 2 tablespoons cold water
½ cup red wine or Bone Stock Salt, to taste
1 teaspoon fish sauce

1. Pierce the spaghetti squash all over with a fork. Cook the squash whole in the microwave for 10 to 15
minutes or in a preheated 375°F oven for 45 minutes to 1 hour.
2. Let the spaghetti squash cool. Cut in half lengthwise. Spoon out the seeds and discard. Scrape out the noo-
dlelike strings with a fork (a fun way to serve this is right in the rind!).
3. Meanwhile, brown the meat, onion, and garlic in a large skillet over medium-high heat, about 10
minutes.
4. Once the meat is cooked, add the mushrooms, wine, and fish sauce.
5. Reduce the heat to medium. Cook for 7 to 10 minutes, until the mushrooms are cooked, stirring occasionally.
6. Add the olives, basil, and oregano. Simmer for 1 to 2
minutes.
7. Mix the kuzu starch with the cold water. Add to
the meat, stirring quickly. Simmer for 1 to 2 more
minutes, until the liquid has completely thickened.
Taste and season with salt if desired. Serve on the
spaghetti squash noodles.

262 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 DIY FRUIT SALAD
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

THAI-INSPIRED STONE FRUITS WITH BALSAMIC

1 cup papaya chunks 1 cup pitted and quartered apricots
1 cup mango chunks 1 cup pitted and halved cherries
1 cup pineapple chunks 1 cup sliced peaches or nectarines
1 cup thinly sliced starfruit 1 to 2 tablespoons well-aged balsamic vinegar
1 teaspoon finely chopped 1 teaspoon finely chopped
Honey-Candied Ginger fresh basil leaves
1 teaspoon finely grated lime zest
1 to 2 tablespoons lime juice and/or RED AND GREEN
strong-brewed, chilled jasmine tea 1 cup watermelon chunks
1 cup strawberries
TROPICAL 1 cup sliced kiwi
1 cup peeled, pitted, and halved lychee 1 to 2 tablespoons fresh
1 cup pineapple chunks lemon juice
1 cup orange segments 1 to 2 teaspoons finely
1 cup sliced banana (see Tips) chopped fresh mint leaves
1 teaspoon finely grated lime zest
1 to 2 tablespoons fresh lime juice

1. Combine the ingredients in a bowl and enjoy!

263 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 KALE CHIPS
PREP TIME COOK TIME SERVES

5 minutes 20-22 minutes 2-4 servings

8 loosely packed cups kale, torn into 1-1½“ pieces, tough stems removed
2 tablespoons extra virgin coconut oil, melted and still warm
¼ teaspoon salt, to taste

1. Preheat oven to 325F.

2. Wash and dry kale. Place in a plastic container or large bowl.
3. Poor warm oil over kale, close container lid, and shake to coat (alternatively, stir to coat in a
bowl or give them a good massage with your hands directly on the baking sheet).
4. Spread out onto a large baking sheet. Sprinkle with salt (careful, it doesn’t take much).
5. Bake for 20-22 minutes, until crispy.

264 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SALMON WITH
MAÎTRE D’ “BUTTER”
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

1 tablespoon finely grated lemon zest (about 1 lemon)

4 large cloves garlic, crushed
²⁄3 cup chopped fresh dill
½ cup minced fresh parsley
½ teaspoon salt
1 cup lard, at room temperature
6- to 8-ounce salmon fillets (as many as desired)

1. Combine the lemon zest, garlic, herbs, and salt with the lard in a small bowl. Mix until well combined.
2. Preheat the oven to 350°F.
3. Prepare a parchment or foil “envelope” for each piece of fish.
4. Place a large sheet of parchment paper or aluminum foil on a rimmed baking sheet. The parchment or
foil should measure a little over twice the length of the fish fillet. (You can also place all of your fillets
in one large parchment envelope. To create an envelope for more than one fillet, place them side by
side and ensure that there is 3 to 4 inches of extra parchmentwidth at the top and bottom.)
5. Place the salmon fillet on the bottom half of the parchment or foil, leaving 3 to 4 inches of space (in
addition to one long side) around it for folding over. Spoon a tablespoonful of herb butter onto each
fillet (you can spread it out or leave it as a ball). Also add approximately 1 tablespoon of water around
the fillets (add 2 tablespoons if placing more than one fillet in each envelope). Fold over the long top
portion of the parchment or foil to cover the fish. Then triple-fold the edges on all three unsealed sides
to form a fully sealed envelope or pocket.
6. Place in the oven (still on the baking sheet) and bake for 20 minutes, until the fish is opaque throughout
and the segments flake apart easily. Be careful when opening the envelopes to avoid steam burns.

265 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SAVORY ROASTED TARO
PREP TIME COOK TIME SERVES

15-20 minutes 25 minutes 2-4 servings

2 pounds fresh taro (8 to 10 small tubers)

3 tablespoons tallow, lard, or duck fat, melted
2 teaspoons dried savory
2 cloves garlic, crushed
½ teaspoon salt

1. Place the whole unpeeled taro tubers in a steamer basket or steamer insert. Bring the water to a boil
and steam for 10 to 15 minutes (depending on the size of the tubers) until you can pierce them easily
with a knife but before they get too soft (think of the firmness of not-quite-cooked potatoes). Remove
from the heat and let cool enough to handle.
2. Meanwhile, place an oven rack 6 to 8 inches from the broiler element, and preheat the broiler on high
for 10 minutes.
3. Peel off the barklike skin of the taro with a paring knife (it should come off fairly easily). Cut the
peeled taro into quarters or ½-inch-thick rounds and place in a large bowl. Pour the tallow, savory,
garlic, and salt over the taro and toss to coat. Spread the taro on a rimmed baking sheet.
4. Broil for 10 minutes, flipping or stirring every 3 to 5 minutes, until browned and slightly crisp on the
outside.

266 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 WILD MUSHROOMS AND
TARRAGON
PREP TIME COOK TIME SERVES

5 minutes 10-13 minutes 2-4 servings

2 tablespoons lard, tallow, duck fat, or bacon fat

1½ pounds wild mushrooms
2 tablespoons chopped fresh tarragon
1 clove garlic, crushed
1 tablespoon fresh lemon juice
¹⁄8 teaspoon salt

1. Heat the lard in a skillet over medium-high heat. Add the mushrooms and cook, stirring occasionally,
until browned, 8 to 10 minutes. If the mushrooms are releasing a lot of water into the skillet and get-
ting soupy, turn up the heat to keep the pan dry.
2. Add the tarragon, garlic, lemon juice, and salt and cook for 2 to 3 more minutes, stirring to incorporate.
Serve!

267 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SUPERFOOD SMOOTHIE
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

½ banana
¼ avocado
1 cup vegetable juice (homemade or store-bought) or water, chilled
2 to 3 cups fresh leafy greens (spinach, kale, lettuce, baby
collards, etc.)
1 teaspoon to 2 tablespoons superfood add-ons: sea vegetables,
desiccated liver or other organs, cubes of frozen liver or other organ meat,
nutritional yeast (make sure it’s gluten-free), coconut milk kefir or yogurt,
high-quality extra-virgin olive oil, fermented cod liver oil, freeze-dried acai
powder, kombucha, or Bone Stock or soft bones left over from making
broth (optional)
1 to 2 tablespoons protein powder (beef isolate, beef plasma isolate, gela-
tin, collagen, insect powder/flour, or a mix)

1. Place all the ingredients except the protein powder in a

blender and blend on high for 1 to 2 minutes, until smooth.
2. Add the protein powder and pulse to incorporate.

268 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BROILED ASPARAGUS
PREP TIME COOK TIME SERVES

5 minutes 6 - 8 minutes 2 - 4 servings

1 pound asparagus, tough ends of spears snapped off and discarded

2 tablespoons avocado oil
¼ teaspoon sea salt or truffle salt

1. osition a rack in the oven 6 inches below the broiler and preheat the broiler on high for 10 to 15
P
minutes.
2. lace the asparagus on prepared rimmed baking sheet. Drizzle with the oil and sprinkle with the salt;
P
toss to combine.
3. Broil for 6 to 8 minutes, until starting to brown.

269 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MEAL PL AN

4
Recipes
270 THE AUTOIMMUNE PROTOCOL
by Dr. Sarah Ballantyne, PhD
 BACON FRUIT CUPS
PREP TIME COOK TIME SERVES

15 minutes 45 minutes to 1 hour 2 servings

12 thick slices bacon

Berries, melon cubes or balls, or fruit of choice

1. Preheat the oven to 375°F. Place 2 (3- to 4-inch) metal sieves upside down in a baking dish.
2. Take 6 slices of bacon and weave 3 slices horizontal and 3 slices vertical in a simple
over-under-over, under-over-under, over-under-over pattern. (Now you’re ready to try
baskets!) Push the slices of bacon tightly together.
3. Carefully transfer your woven bacon to drape over the top of an upside-down metal sieve.
The bacon will want to come unwoven at the corners, so tuck those ends underneath each
other to complete your bowl shape.
4. Repeat for the second bacon cup.
77
3131 DhP ,en y tn all a B h a r a S

5. Bake for 30 minutes, until the bacon is starting to crisp and looks browned.
6. Remove from the oven. Drain the excess bacon fat. Carefully remove each bacon cup from the sieve using
tongs. Using tongs or oven mitts, turn the sieves over. Place the bacon cups right-side-up in the sieves.
7. Place the bacon cups back in the oven and cook for an additional 15 to 25 minutes, until the cups are com-
pletely crisp.
8. Serve warm or cooled, filled with berries, melon cubes or balls, or any other fruit you enjoy with bacon.

TIPS:
1. The cooking time will vary based on how thick
and how fatty the bacon is. Keep a close eye on it
once you get close to the end of the cooking time.
You want the bacon to cook until fully crisp (or
else the bowls won’t hold their shape), but you
don’t want it to burn, either. Some bacon,
especially bacon cured with a lot of sugar or
natural sweeteners like maple syrup, just doesn’t
crisp well; it is likely to burn before it goes crisp,
even when cooked at a lower temperature.

271 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 BACON-APPLE CHICKEN
BURGERS WITH
MAPLE-CRANBERRY SAUCE
PREP TIME COOK TIME SERVES

15 minutes 1 hour 15 minutes 4-6 servings

BACON-APPLE CHICKEN ½ teaspoon salt or truffle salt

BURGERS 1 tablespoon bacon fat or other
8 to 10 ounces bacon cooking fat, if needed
(if using 2½ pounds ground chicken, use
10 ounces bacon)
MAPLE-CRANBERRY SAUCE
1 medium onion, minced
2 cups fresh or frozen cranberries
1 large cooking apple, peeled, cored, and
½ cup grade B maple syrup
minced
¼ cup water
2 teaspoons minced fresh rosemary
2 to 2½ pounds ground chicken

MAPLE-CRANBERRY SAUCE:
1. Combine the cranberries, maple syrup, and water in a small saucepan.
2. Bring to a boil over high heat, then reduce the heat to maintain a simmer.
3. Simmer uncovered for 8 to 10 minutes, stirring
occasionally, until most of the berries have
popped and the sauce has thickened.
4. Transfer to a serving bowl and refrigerate for
at least 1 hour before serving.

BACON-APPLE CHICKEN BURGERS:

5. Place the bacon in a cold skillet, then turn on
the heat to medium-high. Cook, flipping once or
twice, until the bacon is crispy.
6. When the bacon is crispy, remove it from the
pan. Add the onion to the bacon fat in the pan
and sauté for 5 minutes over medium-high heat,
stirring occasionally, until the onion is starting to
soften. Add the apple and rosemary and

272 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 continue sautéing until the onion is browned and both the onion and apple are soft, 5 to 8 more min-
utes. Remove from the pan with a slotted spoon and allow to cool slightly. Do not clean the pan; you
will be using it to cook the burgers.
7. Once the bacon has cooled enough to handle, chop into small pieces (think bacon bit size).
8. Combine the ground chicken, bacon, apple and onion mix, and salt in a bowl. Mix well with your hands
and form into 6- to 8-ounce patties.
9. Preheat the pan over medium heat. If there is no more bacon fat left in the pan, add a tablespoon of
bacon fat or other cooking fat. Fry the patties in the pan, in batches if needed so as not to overcrowd,
until fully cooked, 15 to 25 minutes total, flipping once. To be sure that the meat is fully cooked, check
the internal temperature with a meat thermometer; it should read 160°F.

TIPS:
1. Good cooking apple varieties are Granny Smith, Fuji, and Rome Beauty. They hold their shape when
cooked rather than turning to mush, which yields a nicer texture in the finished burgers.
2. You can also make these burgers with ground turkey or ground pork.

273 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ROASTED
BUTTERNUT SQUASH
PREP TIME COOK TIME SERVES

15 minutes 30-35 minutes 4-6 servings

2 pounds butternut squash

2 tablespoons extra-virgin coconut oil, lard, or duck fat, melted
2 teaspoons chopped fresh
thyme leaves
¼ teaspoon salt

1. Preheat the oven to 425°F. Line a baking sheet with aluminum foil, parchment paper, or a silicone liner.
2. Pierce the squash once or twice with the tip of a knife, then microwave on high for 1 to 2 minutes. (This
makes it easierto peel the squash but is not necessary if you don’t have a microwave.) Peel the squash,
cut in half lengthwise, and scoop out the seeds. Cut the squash into 1 ½-inch chunks. In a large bowl,
toss the squash with the oil, thyme, and salt. Spread out onto the prepared baking sheet.
3. Bake for 30 to 35 minutes, until slightly browned and tender. Shake the pan (or flip the squash chunks)
every 10 minutes during baking.

274 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ROASTED BROCCOFLOWER
AKA ROMANESCO
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

8 cups broccoflower florets and cubed stems (about 2 pounds)

¼ cup avocado oil
6 to 8 cloves garlic, crushed
1 tablespoon finely grated
lemon zest (about 1 lemon)
¼ teaspoon salt or truffle
salt
¼ cup chopped fresh parsley

1. Preheat the oven to 450°F.

2. I n a casserole dish, toss the broccoli (and cauliflower, if using) florets and stems with the avocado oil,
garlic, lemon zest, and salt.
3. oast for 25 to 35 minutes, until the broccoli and cauliflower are fully cooked (it depends on how
R
big the florets are and how soft you like them), stirring once halfway through cooking.
4. Remove the dish from the oven, toss with the fresh parsley, and serve.

TIPS:
1. For a little extra zing, reserve the juice from
the lemon and squeeze over the broccoli right
before serving.
2. Try adding 2 to 3 tablespoons coconut
aminos, switching out the garlic for grated
fresh ginger, and omitting the lemon zest
and parsley.
3. You can also replace this with broccoli or
cauliflower

275 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 TERIYAKI-POACHED TROUT
PREP TIME COOK TIME SERVES

10 minutes + 15 minutes 10-12 minutes 3-5 servings

for marinating

½ cup fresh orange juice

1 teaspoon finely grated orange zest (optional)
¼ cup coconut aminos
2 teaspoons peeled and finely grated fresh ginger
3 or 4 cloves garlic, crushed
3 or 4 (6- to 8-ounce) trout fillets

1. lace a rack high up in the oven so that the surface of the salmon will be 6 to 8 inches away from the top
P
element. Turn the broiler on high (let it preheat about 10 minutes before putting the salmon in the oven).
Coat a rimmed baking sheet with olive oil.
2. Place the salmon fillets skin side down on the oiled baking sheet.
3. Sprinkle with truffle salt and fresh thyme.
4. roil for 8 to 9 minutes, until fully cooked (when segments flake apart easily and salmon is opaque
B
throughout).

276 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CAULIFLOWER “RICE”
PREP TIME COOK TIME SERVES

15 minutes 7-9 minutes 3 - 6 servings

1 small head cauliflower (about 2 pounds)

3 to 4 tablespoons avocado oil or other cooking fat
¹⁄8 teaspoon salt

1. Core the cauliflower and place the florets in a food processor (you may have to do this in
batches). Pulse until chopped to rice-grain size. Alternatively, you can grate the cauliflower
with a box grater. Set aside.
2. Heat 3 tablespoons of the oil in a large skillet or wok over medium-high heat.
3. Add the cauliflower to the pan and cook, stirring frequently, until the cauliflower is cooked
al dente, 6 to 8 minutes. If the rice starts sticking to the pan or the pan looks very dry, add an
additional tablespoon of coconut oil.
4. Stir in salt and cook for 1 minute.
5. Enjoy!

277 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 TUNA SALAD WRAP
PREP TIME COOK TIME SERVES

10 minutes - 1-2 servings

1 (5-ounce) can albacore tuna 2 tablespoons finely diced red onion

(preferably no salt added), drained 1 stalk celery, finely diced
½ avocado, peeled, pitted, and diced 1 tablespoon fresh lemon juice
2 teaspoons capers, minced Pinch of ground turmeric
3 tablespoons chopped Pinch of salt, plus more to taste
Green Tea and Garlic Pickles Large lettuce leaves, for serving

1. Combine the tuna, avocado, capers, pickles, red onion, celery, lemon juice, turmeric, and salt. Mix to
combine (minimally to keep it chunkier, or more thoroughly to make a smoother tuna salad, depending
on your preference). Taste and season with additional salt, if desired.
2. Carefully slide a knife through the rib of each lettuce leaf to remove it (this makes it easier to fold the
lettuce leaves into wraps). Add a spoonful of tuna salad and wrap the lettuce around it.

278 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 PLANTAIN CRACKERS
PREP TIME COOK TIME SERVES

10-15 minutes 60-80 minutes 6-10 servings

2 large or 3 medium green plantains

½ cup coconut oil, melted
½ teaspoon salt, to taste

1. Preheat the oven to 300°F. Line a 13-by-18-inch rimmed baking sheet with parchment paper or a
silicone liner. Make sure that the parchment goes right up to each edge of the pan.
2. Peel the plantains and place in a food processor with the coconut oil and salt. Process until a complete-
ly smooth puree forms, 3 to 5 minutes, turning off the processor and scraping down the sides at least
once. (You should have about 2 cups of puree.)
3. Pour the batter (it should look like hummus) onto the prepared baking sheet. Use a rubber spatula to
smooth it out and cover the entire sheet uniformly. The batter should be about ¹⁄8 inch thick.
4. Bake for 10 minutes. Remove from the oven and score the batter with a pastry wheel, pizza cutter, or
pastry scraper. You can make whatever size crackers you like. The crackers will pull away from each
other slightly while cooking and will shrink up a bit, but not much.
5. Return the pan to the oven and bake for 50 to 70 minutes, until the crackers are dark brown.
6. Remove from the oven and let cool slightly in the pan. Move to a cooling rack (you will probably be
moving fairly big pieces of several crackers stuck together). Once completely cool, you can break apart
any crackers that are stuck together.
7. Store in an airtight container at room temperature. Enjoy!

279 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 “CREAM” OF
BROCCOLI SOUP
PREP TIME COOK TIME SERVES

5-10 minutes 12-15 minutes 4 servings

2 pounds broccoli
2 small avocados
4 cups Bone Stock
¼ teaspoon ground mace
Salt, to taste

1. Wash and cut the broccoli into florets. Slice the stems (peel them if they are tough). Peel and pit the
avocados and cut the flesh into medium-sized chunks.
2. Bring the Bone Stock to a simmer in a saucepot over medium-high heat.
3. Add the broccoli and cook for 7 to 8 minutes, until dark green and tender.
4. Reduce the heat to low. Add the mace and avocado to the pot. Cook for 3 to 4 more minutes, until the
avocado has warmed.
5. Purée with an immersion blender (or in a blender or food processor). Taste and add salt, if desired.
Enjoy!

280 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 TARRAGON ROASTED PORK
PREP TIME COOK TIME SERVES

15 minutes 10 minutes 4 servings

3 tablespoons dried tarragon

2 teaspoons salt
1 (4- to 5-pound) pork roast (leg or loin)

1. Preheat the oven to 350°F.

2. Combine the tarragon and salt in a spice grinder or mortar and pestle and grind until it’s a fine powder.
3. Place the roast on the rack of a roasting pan. Pat dry with paper towels. Rub the tarragon and salt mix-
ture over the entire surface of the roast. Insert an oven-safe meat thermometer.
4. Roast for 20 minutes per pound, until the internal temperature reaches a minimum of 145°F.
5. Let the roast rest for 10 minutes before carving.

281 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 50/50/50 BURGERS
PREP TIME COOK TIME SERVES

20-30 minutes 20-25 minutes 6-12 servings

1 pound bison liver

1 pound bacon
1 pound ground beef
2 tablespoons good cooking fat or oil, such as tallow, lard, or coconut oil,
for pan-frying

1. Grind the liver and bacon separately using a meat grinder or food processor.
2. In a large bowl, combine the ground liver and bacon with the ground beef. Form whatever size
patties you want, typically 4 to 8 ounces each. (The liver makes the meat mixture a little sticky. If it’s
too sticky, try wetting your hands with cold water before forming the patties.)
3. TO GRILL: Preheat a grill pan or a gas or charcoal grill to medium- high heat. Place the patties on the
hot grill. Grill for 6 to 8 minutes per side, or until cooked to your liking.
4. TO PAN-FRY : Heat a couple tablespoons of cooking fat over medium-high heat. Place the patties in
the hot pan. Cook for 8 to 12 minutes per side, or until cooked to your liking.
5. TO BAKE: Preheat the oven to 400°F. Place the patties on a deep-rimmed baking sheet or roasting
pan. Bake for 18 to 22 minutes, or until cooked to your liking.
6. Let the burgers rest for 5 minutes before eating.

282 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 PORTOBELLO “BUNS”
PREP TIME COOK TIME SERVES

5 minutes 3- 5 minutes 4-6 servings

3 tablespoons avocado oil

3 tablespoons balsamic vinegar
4 to 6 portobello mushroom caps, stems

1. Mix the avocado oil and balsamic vinegar in a small bowl. Use a marinating or pastry brush to brush
both sides of each mushroom cap, being most generous on the lamella (gill) side.
2. Grill for 3 to 5 minutes per side, until grill marks form and the mushrooms are fully cooked.

283 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 PALEO FRENCH FRIES (AIP)
PREP TIME COOK TIME SERVES

10-15 minutes 20 minutes 8 servings

2 pounds green plantains or starchy root vegetable

(sweet potatoes, yam, lotus root, taro root, celery root, or parsnip)
lard or other fat, for deep frying
2 teaspoon sea salt

1. Peel your root vegetables if they have a tough skin; otherwise, simply clean them. Cut the root
vegetables into French fry−like strips (2 to 4 inches long and ½ inch thick), ½-inch thick wedges,
or ½-inch-thick rounds. Rinse and drain on paper towels.
2. Heat the lard to 360°F in a countertop deep-fryer or heavy-bottomed pot over medium heat
with a deep- fry thermometer attached to the side. Use enough fat to fill your deep-fryer to the
fill line or to have 2 inches of fat in the bottom of your pot.
3. Cook the vegetables in small batches so as to not overcrowd, for 3 to 7 minutes, until browned
and crisp on the outside.
4. Allow to dry on a paper towel, tea towel, or newsprint-lined plate or rimmed baking sheet.
Sprinkle with the salt while still warm.

TIPS:
The best root vegetables for making French fries are those with a naturally low water content. Less
starchy vegetables like rutabaga, turnips, carrots, and beets tend not to crisp up on the outside and are
better if left to other cooking methods. Even some varieties of sweet potato work better than others
due to the water content (my favorites are purple sweet potatoes and Japanese sweet potatoes).
5. If using yuca, a little extra prep work is required.
Peel and cut into rectangular “fries,” wedges, or
rounds, then soak in water in the fridge for 24
hours; this reduces the cyanogenic glycoside con-
tent. Drain and rinse. Then boil in water for
10 minutes. Drain well and pat dry with paper tow-
els before deep-frying.
6. If using more than one kind of root vegetable, cook
the vegetables in separate batches, since
different root vegetables require slightly
different cooking times.

284 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GUACAMOLE
PREP TIME COOK TIME SERVES

- -
3-4 servings

1½ large ripe avocados, or 2 smaller avocados

½ cup finely chopped fresh cilantro
1 tablespoon lime juice
½ teaspoon sea salt or truffle salt

1. Cut the avocados in half and scoop the flesh into a small bowl.
2. dd the remaining ingredients, mash with a fork to thoroughly mix, and serve. Store leftovers
A
in the fridge for up to a week.

285 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SIMPLE GRILLED STEAK
WITH RHUBARB CHUTNEY
PREP TIME COOK TIME SERVES

15 minutes 30-40 minutes 4 servings

RHUBARB CHUTNEY: ¼ teaspoon peeled and grated fresh ginger

8 ounces rhubarb, cut into ½ teaspoon ground cinnamon
½-inch-thick slices Pinch of ground cloves ¼ teaspoon salt
¼ medium yellow onion, finely diced
½ apple, peeled, cored, and grated STEAK:

1½ teaspoons finely grated orange zest 4 (4- to 8-ounce) steaks

2 tablespoons fresh orange juice 1 to 2 tablespoons Steak Spice
2 tablespoons coconut water vinegar

RHUBARB CHUTNEY:
1. Combine all the chutney ingredients in a saucepan.
2. Bring to a simmer over medium-high heat. Reduce the heat
3. to medium-low and simmer uncovered until thick, approximately 30 minutes.
4. Serve warm or chill for 1 hour to serve cold.

STEAK:
5. Pat the steaks dry with paper towels and season with the steak
spice.
6. Preheat a grill pan or a gas or charcoal grill. Once hot, place the
steaks on the grill. Grill for 3 to 5 minutes per side, depending on
how you like your steak cooked and how thick the steaks are.
7. Let the steaks rest for at least 5 minutes before serving.

286 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 ROASTED SWEET POTATO
PREP TIME COOK TIME SERVES

10 minutes 40 minutes 4-8 servings

2 pounds sweet potatoes, peeled and cut into ½-inch thick circles
(or semicircles, if big around; you can also cut thick wedges
to make sweet potato fries)
2 tablespoons extra-virgin coconut oil, melted
¼ teaspoon salt, to taste (optional)

1. Preheat the oven to 350°F. Line a rimmed baking sheet with aluminum foil or parchment paper,
or use a silicone baking mat.
2. Place the sweet potato slices in a large bowl. Toss with the coconut oil and salt until evenly coated.
Arrange the slices in a single layer on the prepared baking sheet.
3. Bake for 25 minutes, then remove from the oven and turn each slice over.
4. Bake for another 15 minutes. Enjoy!

287 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 TARO HASH
PREP TIME COOK TIME SERVES

15 minutes 30-40 minutes 3-4 servings

1 pound taro roots

4 thick slices bacon, chopped
1 clove garlic, crushed
2 tablespoons chopped green onion or chives

1. Place the whole taro roots in a steamer insert with 1 inch of water in the saucepot underneath. Bring
to a boil and steam for 10 to 15 minutes, until the taro is soft enough to pierce easily with a knife (but is
not mushy). Remove the steamer insert from the pot and allow the taro to cool enough to handle.
2. Place the chopped bacon in a skillet, then turn on the heat to medium-high. Sauté the bacon, stirring
occasionally, until browned, 7 to 8 minutes.
3. Meanwhile, peel the dark brown skin off the steamed taro (it should come off easily). Cut the taro into
¼-inch dice.
4. Add the taro to the skillet with the bacon. Continue to sauté, gently stirring occasionally, until the taro
has browned, 10 to 15 minutes. Add the garlic and green onion and cook for 2 to 3
minutes more. Serve.

TIPS:
1. You can steam the taro root ahead of time to make this dish quicker to prepare in the morning.

288 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 LEMON AND THYME BROILED
SALMON WITH BLOOD
ORANGE SALSA
PREP TIME COOK TIME SERVES

30 minutes 10-12 minutes 4 -8 servings

SALSA SALMON
2 pounds blood oranges, 4 to 6 (6- to 8-ounce) salmon fillets
segmented (see Tips) 1 tablespoon finely grated
Finely grated zest of 1 lime lemon zest (about 1 lemon)
Juice of 1 lime ¼ cup fresh lemon juice
½ medium red onion, diced 1 tablespoon chopped
3 stalks celery, diced fresh thyme
¼ cup chopped fresh ½ cup white wine, fresh
cilantro orange juice, or apple juice

1. lace a rack high up in the oven so that the surface of the salmon will be 6 to 8 inches away from the
P
top element. Turn the broiler on high (let it preheat about 10 minutes before putting the salmon in the
oven). Coat a rimmed baking sheet with olive oil.
2. Place the salmon fillets skin side down on the oiled baking sheet.
3. Sprinkle with truffle salt and fresh thyme.
4. roil for 8 to 9 minutes, until fully cooked (when
B
segments flake apart easily and salmon is opaque
throughout).

TIPS:
5. To segment an orange, use a sharp paring knife
to cut off the top and bottom. Lay the orange on
a cutting board and cut off the peel all the way
around. Then, holding the orange in your hand,
use the knife to carefully cut out each segment
by cutting down one side of the segment close to
the membrane and then twisting the knife to pry
the segment off the membrane on the other side.

289 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SUPERFOOD SMOOTHIE
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

½ banana
¼ avocado
1 cup vegetable juice (homemade or store-bought) or water, chilled
2 to 3 cups fresh leafy greens (spinach, kale, lettuce, baby
collards, etc.)
1 teaspoon to 2 tablespoons superfood add-ons: sea vegetables,
desiccated liver or other organs, cubes of frozen liver or other organ meat,
nutritional yeast (make sure it’s gluten-free), coconut milk kefir or yogurt,
high-quality extra-virgin olive oil, fermented cod liver oil, freeze-dried acai
powder, kombucha, or Bone Stock or soft bones left over from making
broth (optional)
1 to 2 tablespoons protein powder (beef isolate, beef plasma isolate,
gelatin, collagen, insect powder/flour, or a mix)

1. Place all the ingredients except the protein powder in a

blender and blend on high for 1 to 2 minutes, until smooth.
2. Add the protein powder and pulse to incorporate.

290 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 SARDINE SALAD
PREP TIME COOK TIME SERVES

10 minutes - 2 servings

2 tablespoons extra-virgin olive oil 1 tablespoon chopped fresh tarragon

1 teaspoon finely grated lemon zest 2 stalks celery, finely diced
Juice of 1 lemon 2 (4-ounce) cans sardines
1 tablespoon capers packed in olive oil, drained
2 tablespoons chopped fresh parsley 6 to 10 cups arugula or mustard greens

1. In a bowl, mix together the olive oil, lemon zest and juice, capers, parsley, tarragon, and celery.
2. Toss the sardines with the dressing. Place the arugula on 2 serving plates and pour the sardine mixture
over the top.

291 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GREEK-INSPIRED
LAMB CHOPS
PREP TIME COOK TIME SERVES

5-10 minutes 8-16 minutes 4-6 servings

3 cloves garlic, crushed

1 tablespoon finely grated lemon zest (about 1 lemon)
1 tablespoon minced fresh oregano
¼ teaspoon salt
2 pounds lamb chops (rib or loin)

1. Position an oven rack so that your lamb chops will be about 6 inches from the top element in your
oven. Preheat the broiler on high for 10 minutes while you prepare the lamb.
2. Combine the crushed garlic, grated lemon zest, oregano, and salt.
3. Pat the lamb chops dry with paper towels and place on a roasting pan. Rub the seasoning mix all over
the top and bottom of the chops.
4. Broil for 4 to 8 minutes per side (depending on the thickness of your lamb chops), until the internal
temperature reaches 145°F for medium-rare or 160°F for medium.
5. Let the chops rest for 5 minutes.
6. Enjoy!

292 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MINT PESTO
ZUCCHINI “PASTA”
PREP TIME COOK TIME SERVES

15 minutes, + 1 hour to 15-18 minutes 2-4 servings

salt the zucchini

2 pounds zucchini (about 3 medium)

1 tablespoon salt
8 to 10 cloves garlic, unpeeled
2 tablespoons extra-virgin olive oil
2 tablespoons chopped fresh mint
2 to 3 tablespoons lard, coconut oil, or bacon fat

1. Slice the zucchini into long, thin noodles with a spiral vegetable slicer, mandoline slicer, or julienne
peeler. (With some patience, you can also julienne long strips of zucchini with a knife.) Sprinkle
liberally with the salt and place in a colander in the sink for 1 hour (this helps remove excess water so
that the zucchini holds together better once cooked).
2. Meanwhile, make the mint pesto: Place the whole, unpeeled garlic cloves in a dry pan. Heat over
medium-high heat, stirring or shaking the pan occasionally, until the papery peel of the garlic browns
and starts to flake off, about 10 minutes.
3. Remove the garlic from the pan and let cool enough to handle. Remove the peel. Place the garlic, olive
oil, and mint in a mini food processor and pulse until you get a
pastelike texture, or grind the ingredients to a paste by hand
using a mortar and pestle.
4. Rinse the zucchini noodles thoroughly. Drain and invert onto pa-
per towels or a clean kitchen towel. Place another kitchen towel
or paper towels on top and gently press to remove as much water
as possible.
5. Heat the lard in a large skillet or wok over medium-high heat.
Add the zucchini noodles once the pan is hot. Cook, stirring gen-
tly but frequently, until the zucchini is cooked al dente,
6. 5 to 8 minutes. Keep the heat high enough that any liquid
released by the zucchini is evaporating. If a lot of liquid
accumulates in the bottom of the pan, turn up the heat.
7. Remove from the heat and toss with the mint pesto. Serve.

293 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 DESSERTS

294 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 HONEY-CANDIED GINGER
PREP TIME COOK TIME SERVES

15 minutes, 1 hour 15 minutes 10-20 servings

½ pound fresh ginger

2 cups water
1¼ cups honey

1. Peel the ginger and slice as thinly as possible (a mandoline slicer is helpful but not essential).
2. Bring the ginger and water to a boil in a pot over high heat. Cover and reduce to a simmer for 30 min-
utes, then uncover and continue to simmer for another 10 to 15 minutes, until tender. Make sure that
the pot doesn’t boil dry (add some water if it does).

3. Drain all but ¼ cup of the water from the pot. Add the honey to the pot. Simmer uncovered over low
heat for another 30 to 40 minutes, until the ginger has turned darker in color and slightly translucent.
Stir occasionally to make sure that it doesn’t burn.
4. Remove from the heat. Store the candied ginger the syrup in the fridge for up to several months.

295 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CAROB BROWNIE BITES
PREP TIME COOK TIME SERVES

20 minutes 9-10 minutes 12-16 cookies

1 large green plantain 2 teaspoons vanilla extract

¼ cup palm shortening ¹⁄8 teaspoon baking soda
2 tablespoons extra-virgin coconut oil Pinch of salt
2 tablespoons molasses Pinch of ground cinnamon
½ cup carob powder ¾ teaspoon baking soda
2 tablespoons tapioca flour ½ teaspoon salt
2 tablespoons arrowroot powder

1. Preheat the oven to 350°F.

2. Peel the green plantain (see page 57). Place the plantain, palm shortening, coconut oil, and molasses
in a food processor and process for 2 to 3 minutes, until it is a smooth puree.
3. Add the remaining ingredients and process until combined.

4. Using your hands, roll the dough into 1 ½-inch balls and place on a baking sheet. Use your palm or the
bottom of a glass to flatten the dough balls to ½ inch thick.
5. Bake for 9 to 10 minutes, until the balls are just starting to brown on the bottom and edges.
6. Let cool and enjoy.

296 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 GINGERBREAD COOKIES
PREP TIME COOK TIME SERVES

20 minutes + 1 hour 12 minutes 2 dozen cookies

chill time

¼ cup lard or palm shortening, softened 2 cups Otto’s Naturals cassava flour,
¼ cup muscovado sugar divided use

½ cup plus 2 tablespoons molasses 2 tablespoons plus 2 teaspoons water

¹⁄8 teaspoon mace

3
⁄4 teaspoon baking soda mixed in 1 tablespoons
water
½ teaspoon ground cinnamon
1 teaspoon ground ginger
TO ROLL:
½ teaspoon ground cloves
1 tablespoons maple sugar
¼ teaspoon sea salt
2 teaspoon ground cinnamon

1. In a large mixing bowl, cream together the lard and sugar. Add the molasses and blend to combine.

2. In a small bowl, mix together the mace, cinnamon, ginger, cloves, salt, and ½ cup of the cassava flour.
3. Add to the bowl with the molasses mixture. Blend until combined.

4. Add the remaining cassava flour, ¼ cup at a time, alternating with small amounts of the water and
mixing well after each addition.
5. Add the mixture of baking soda and water and stir well to fully combine. Cover and refrigerate
for 1 hour.
6. When ready to bake: Preheat oven to 350°F.
Line a baking sheet with parchment paper.
In a small bowl, combine the maple sugar and
cinnamon. Shape dough into 1- to 1-½-inch balls
and roll in the cinnamon mixture. Place on the
prepared baking sheet, then flatten each cookie
with a fork, to about ½-inch thickness. Bake 10-12
minutes or until edges are lightly browned and
centers are set. Cool completely on the cookie
sheet, then enjoy!

297 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 APRICOT-GINGER FRO-YO
PREP TIME COOK TIME SERVES

20 minutes + chilling - 1 quart

3 cups sliced fresh apricots

1½ cups Coconut Milk Yogurt
¼ cup honey
3 tablespoons chopped candied ginger

1. Combine the apricots, coconut milk yogurt and honey in a blender. Blend until completely smooth.
Chill in the fridge, at least 1 hour.
2. Stir in chopped candied ginger and place the chilled yogurt in an ice cream maker and churn following
the manufacturer’s directions. Enjoy! Store any leftovers in the soft zone of your freezer.

298 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CAROB GANACHE
MINI TORTES
PREP TIME COOK TIME SERVES

5 minutes 5 minutes + chilling time 2 - 4 servings

²⁄3 cup full-fat coconut milk

¹⁄3 cup extra-virgin coconut oil
2 tablespoons vanilla extract or 1½ teaspoons
vanilla powder
¹⁄3 cup carob powder
Dash of ground cinnamon
Berries for serving, if desired

1. Bring the coconut milk, coconut oil, and vanilla to a low simmer in a small saucepan over medium-low
heat. If using vanilla extract, let simmer 5 to 10 minutes to burn off the majority of the alcohol from
the vanilla, stirring frequently.
2. Pour the coconut milk into a blender. Add the carob and cinnamon. Blend 30 seconds to 1 minute to
thoroughly combine.
3. Pour into individual ramekins, silicone molds, or a large serving dish. Chill until set, 3 to 4 hours.
4. Enjoy plain or serve with berries

299 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 CARAMEL APPLES
PREP TIME COOK TIME SERVES

10 minutes, 30 minutes 8 - 10 apples

plus an hour to cool

1 cup honey
1 cup coconut cream, homemade or store-bought
Dash of sea salt
8 to 10 apples, chilled

1. Combine the honey, coconut cream, and salt in a medium, heavy-bottomed pan. Whisk to thoroughly
combine. Attach a candy thermometer to the side of the pan.
2. Turn the element on to medium-low heat. Heat the mixture until it reaches 245°F (don’t go over 248°F).
No need to stir. Around 220°F, it will start to bubble . . . if it looks like it’s going to bubble over, stir a lit-
tle to pop some of the bubbles. This should take 20 to 30 minutes and is pretty hands off, so be patient.
3. Once it reaches 245°F, remove from the heat. Let the caramel cool down to under 200°F before dipping
the apples. Around 180°F works best for a thick coating.
4. While waiting for the caramel to cool, skewer the apples with the ice pop sticks. And line a rimmed
baking sheet with wax paper, parchment paper, or a silicone baking mat and grease the paper or liner.
5. Once the caramel is cool, dip the apples in the caramel to evenly coat. Place the apples on the prepared
baking sheet and then place the baking sheet in the fridge for the caramel to harden.
6. Let the apple set for at least an hour, if not two or three before peeling them off the sheet. (I know it’s
difficult to wait!)

S P E C I A L E Q U I P M E N T:
1. 8 to 10 ice pop sticks or cake pop sticks

300 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 STRAWBERRY-RHUBARB
COBBLER
PREP TIME COOK TIME SERVES

20 minutes, 30 minutes 10 servings

FOR THE FILLING FOR THE BISCUITS

1 ½ pounds rhubarb, chopped 1 ½ cups of cassava flour
½ cups of maple syrup 1 teaspoon baking soda
3 tablespoons arrowroot powder 1 teaspoon cream of tartar
3 tablespoons water ¼ teaspoon salt
1 ½ pounds strawberries, sliced ½ teaspoon cinnamon
½ teaspoon vanilla 4 tablespoons lard, cold
2 teaspoon orange zest 3
⁄4 cup coconut cream
1 teaspoon cinnamon
1 tablespoon maple sugar

1. MAKE THE BISCUITS: In a large bowl, combine the cassava flour, baking soda, cream of tartar,
salt, and cinnamon.
2. Add the lard, then use a whisk or two knives to cut the lard into the cassava flour mixture until it
resembles dry oatmeal; the largest pieces of lard should be no bigger than peas.
3. Add coconut cream and mix until the dough is soft and leaves the side of the bowl. If the dough is still
dry or crumbly, add water a tablespoon at a time
until the dough comes together.

4. Roll out dough 3⁄4 inches thick. Use a 2 inches

biscuit cutter to make into 10-12 biscuits.
5. Preheat oven to 400°F.
6. MAKE THE FILLING: In a large saucepan
set over medium-high heat, add the rhubarb and
maple syrup. Bring to a simmer, then lower heat
to medium and cook until rhubarb is soft but not
mushy, about 8 minutes.
7. In a small bowl, mix together the arrowroot
powder and water. Add to the rhubarb and stir
until thickened, about 1 minute. Remove pan

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by Dr. Sarah Ballantyne, PhD
 from heat and fold in the strawberries, vanilla, and orange zest. Pour into a 9-by-9-inch baking dish.
8. Arrange the biscuits on top of the filling.
9. In a small bowl, combine the cinnamon and maple sugar. Sprinkle evenly over the tops of the biscuits.
Bake for 20 minutes or until filling is bubbling and the biscuits have browned lightly. Let cool at least
15 minutes before serving. Store leftovers in the fridge for up to a week.Mix cinnamon and maple
sugar together and sprinkle over the top of each biscuit. Bake 20 minutes. Let cool at least 15 minutes
before serving. Store leftovers in the fridge for up to a week.
TIPS:
1. These biscuits are delicious on their own too! Arrange on a rimmed baking sheet lined and bake in a
400°F oven for 15 minutes. Make savory biscuits by replacing cinnamon and cardamom with 2 to 3
tablespoons chopped fresh herbs.

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by Dr. Sarah Ballantyne, PhD
 Want More Recipes?
Get 200+ AIP friendly
recipes plus tons
of AIP resources in
The Paleo Approach
CookBook

LEARN MORE

The Paleo Approach Cookbook

The Paleo Approach Cookbook is the National bestselling companion cookbook to The Paleo Approach! The
Paleo Approach Cookbook is over 400 pages and includes over 200 recipes, all strict autoimmune protocol
(AIP), and lots of resources (over 100 pages worth!) to help you be successful in the kitchen while you tackle
the diet recommendations in The Paleo Approach. With such a huge number of recipes (that each include
cook time, prep time, servings, tips, variations, nutrition facts, FODMAP alerts), as well as hundreds of recipe
variations, there’s something for everyone! The Paleo Approach Cookbook also includes a summary of the
diet, cooking guides, kitchen How-Tos, shopping lists, food storage guides, kitchen tool essentials, cooking
glossary of terms, time management strategies, how to read labels, recipe Top Ten, alphabetical Yes-
No-Maybe-So list of foods, 6 one-week meal plans (two of which are low-FODMAP) and MORE!
Click here to learn more!

303 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 RECOMMENDED
AIP RESOURCES
The AIP Lecture Series
The Autoimmune Protocol Lecture Series is a 6-week video-
based, self-directed online course that will teach you the scientific
foundation for thediet and lifestyle tenets of the Autoimmune
Protocol. Think of this course as going to college for your health!

THE AIP LECTURE SERIES FEATURES:

•• 42 video lectures (totaling 16 hours!), all taught LEARN MORE
by Dr. Sarah Ballantyne, PhD
•• action steps to help you go from theory to practice
•• dozens of printable guides
•• daily self-discovery exercises to reinforce and refine implementation
•• an online forum to connect with other students and ask questions
•• guided discussions in the online forum
•• weekly FAQ videos by Dr. Sarah Ballantyne, PhD in the online forum
•• recommended reading for every topic

•• interactive quizzes to test your knowledge

The Paleo Approach

The Paleo Approach is the New York Times bestselling complete guide to
using diet and lifestyle to manage autoimmune disease and other chronic ill-
nesses. With over 400 pages of scientific explanations of the why’s, what’s,
and how’s behind diet and lifestyle recommendations to help regulate the
immune system and provide the body with the opportunity to heal. This en-
cyclopedic resource also contains tons of practical information including tips
for transitions, working with your doctor, medical test and treatments that
might be helpful, troubleshooting, and when and how to reintroduce foods.
This book goes into scientific detail, while keeping explanations accessible
and fun to read, and includes over 1200 scientific references. This is the book
for people who want to understand the contemporary science behind how the
food we eat as well as how we live our daily lives together impact our bodies
to either promote health or facilitate disease.
LEARN MORE

304 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 The Healing Kitchen
Achieving health through nutritious food choices has never been simpler nor
more delicious thanks to The Healing Kitchen! This cookbook makes healing
using the Autoimmune Protocol completely accessible to everyone, regard-
less of your budget, time limitations, or access to specialty grocers. Armed
with more than 175 budget-friendly, quick and easy recipes made with
everyday ingredients, you get to minimize time and effort preparing healthful
foods without sacrificing flavor! Straightforward explanations and a com-
prehensive collection of visual guides will teach you which foods are the best
choices to mitigate chronic illnesses, including autoimmune disease. Real-
life practical tips on everything from cleaning out your pantry and easy in-
gredient swaps to reinventing leftovers and DIY flavor combinations will help
you go from theory to practiceeffortlessly. Even better, twelve 1-week meal
plans with shopping lists takes all the guesswork out of your weekly trip to the
LEARN MORE
grocery store!

Paleo Principles
Paleo Principles is the most comprehensive resource to date for those seek-
ing a scientifically founded nutritional approach to optimal health. In her
signature approachable yet scientifically detailed style, Dr. Sarah Ballantyne,
PhD, has laid a complete foundation for understanding the principles of the
Paleo template in order to inform and empower your day-to-day choices.
Combined with an unprecedented collection of practical strategies, tips, and
visual guides, plus more than 200 delicious recipes and twenty meal plans
for diverse health goals, this book is a one-stop-shop for nutrition nerd,
health nut, and gourmand alike. With the perfect balance of detailed expla-
nations, accessible summaries of actionable information, and visual guides,
Paleo Principles provides everything you need to achieve your best health.
LEARN MORE

305 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD
 MORE RESOURCES
COACHING HEALTH TRACKERS
••AIP Certified Coach directory ••Oura Ring
••SAD to AIP in Six
HOME THERAPIES
••AIP Reset
••Joovv
PANTRY INGREDIENTS,
SNACKS AND TREATS AIP COOKBOOKS
••One Stop Paleo Shop ••The Paleo Approach Cookbook
••ShopAIP by Sarah Ballantyne, PhD

••Thrive Market ••The Healing Kitchen

by Sarah Ballantyne, PhD
••Sweet Apricity & Alaena Haber, OTC
••Power Balls ••The Autoimmune Paleo Cookbook
••Epic Bars, Broth and Animal Fats by Mickey Trescott, NTP

••Tropical Traditions ••Alternative Autoimmune Cookbook

by Angie Alt, NTC
MEAL DELIVERY
••Nourish by Rachael Bryant
•• Paleo On The Go
••Simple French Paleo
by Sophie Van Tiggelen
MEAL PL ANNING
••He Won’t Know It’s Paleo
•• Real Plans
by Bre’anna Emmitt

QUALIT Y MEAT ••The Autoimmune Protocol Made Simple

••ButcherBox
by Sophie Van Tiggelen

••The Nutrient-Dense Kitchen

••US Wellness Meats by Mickey Trescott, NTP

••GrassFed Traditions
••Pasturebird AIP BLOGGERS, MEET-UPS
& OTHER RESOURCES
FOOD-BASED SUPPLEMENTS ••AIP Community
••Vital Proteins Liver Pills ••The Paleo Mom Community
••Vital Proteins Collagen Peptides
••Vital Proteins Collagen Veggie Blend
••Dr. Ron’s Ultra-Pure Organ Delight

306 THE AUTOIMMUNE PROTOCOL

by Dr. Sarah Ballantyne, PhD