Autoimmune Protocol
Quick-Start Guide
The Autoimmune Protocol (AIP) has been around since 2012 and there are various sources for
protocol information, both online and in print. Some resources contain inaccurate information
or are simply out of date. Before beginning, understand that the Autoimmune Wellness
website is the best and most accurate public resource for information about AIP, because it
adheres to the latest updates and research as taught to AIP Certified Coach Practitioners and
is able to be updated as changes are announced.
This guide will teach you the basics you need to know to get started with AIP, as well
as link to resources for further learning or to assist in preparing to begin. This guide has
been updated as of January 2024 and reflects the most recent updates to the Autoimmune
Protocol.
What is the Autoimmune Protocol?
The Autoimmune Protocol (also known as “Autoimmune Paleo”, “The Paleo Approach”, or
“AIP”) is a science-based elimination and reintroduction diet and lifestyle protocol. It focuses
on repairing gut health, balancing hormones, and regulating the immune system. The dietary
component includes removing food-driven sources of inflammation and restoring nutrient
density, while the lifestyle component includes approaches to sleep, stress management,
movement, and connection (both with humans and nature), in order to help best manage
autoimmune disease.
AIP has been used successfully alone or in combination with conventional treatments,
depending on a person’s needs. Medical research into the efficacy of AIP has been performed
with patients having Hashimoto’s thyroiditis, rheumatoid arthritis, Crohn’s disease, ulcerative
colitis, eczema, and psoriasis, with more publications coming soon.
Please note, it is important to speak with your doctor or other medical providers before going
through any dietary changes. These materials are for inspiration and informational use only—
they should not be considered medical advice.
Autoimmune Wellness © 2024 All Rights Reserved
No unauthorized copying, editing, or distribution
The three phases of AIP
Transition Phase
Transition is the process of moving one’s diet to the elimination phase, with a focus on
nutrient-density. Some people transition slowly, removing foods one or two at a time over
a period of weeks or even months, while others transition quickly, like over a weekend. In
general, taking the time to make a slow, prepared transition to the elimination diet is best for
most people.
Elimination Phase
Elimination is the period following full transition, when the person is only eating foods
compliant with the elimination phase. The focus is to maintain the food eliminations while
concentrating on nutrient-dense additions, with a goal to maximize healing. Elimination needs
to be 30 days at a minimum for everyone, as this cleans the slate for a clear reintroduction
process. For most, 60-90 days in Elimination is best and allows for the most healing.
Reintroduction Phase
Reintroduction begins after a person has spent 30-90 days fully compliant in the elimination
phase and has had measurable improvements in their symptoms from their baseline as
evidenced from tracking and journaling (and/or lab testing). Ideally, there will be relief of
symptoms. The goal of the reintroduction phase is to determine an individualized, sustainable
(both practically and socially), and nutrient-dense diet. It should be the least-restrictive diet
that gives them the best health.
The elimination phase: Two variations
Originally, the Autoimmune Protocol was conceived as a standard elimination protocol and
that is what has been implemented for years both by individual wellness-seekers and medical
researchers in the AIP intervention studies. This original version has not changed, but is now
called AIP Core Elimination.
In 2024, the Autoimmune Protocol was updated to include a second option for the elimination
protocol, this one modified to include a more expansive list of foods as indicated by the results
of medical research and the clinical experience of practitioners implementing AIP with their
clients and patients for over a decade. This new, less restricted version is called AIP Modified
Elimination.
Whether a person decides to embark on the AIP Core or AIP Modified elimination protocols
is dependent on their practitioner guidance, health conditions, disease severity, ability to
implement, cooking skill or ability, food access or budget, family support, time, and other
factors.
Autoimmune Wellness © 2024 All Rights Reserved
No unauthorized copying, editing, or distribution 2
AIP Core Elimination AIP Modified Elimination
Foods to Avoid: Foods to Avoid:
• Grains (including ingredients derived • Cereal grains (except rice)
from them) • Gluten
• Gluten • Dairy (except ghee)
• Pseudo-grains and grain-like substances • Eggs
• Dairy • Nightshades (including spices derived
• Eggs from them)
• Legumes • Soy
• Nightshades (including spices derived • Tree nuts and peanuts (including
from them) ingredients derived from them)
• Processed vegetable oils • Nonnutritive sweeteners and sugar
• Nuts and nut oils alcohols
• Seeds (including oils and spices derived • Processed food chemicals and
from them) ingredients
• Nonnutritive sweeteners and sugar • Alcohol
alcohols
• Processed food chemicals and
ingredients
• Alcohol
Nutrient-dense additions
One leading theory for the efficacy of the Autoimmune Protocol relates to the nutrient-density
of the overall diet. Therefore, both AIP Core Elimination and AIP Modified Elimination call for
adding in extra nutrient-dense foods that are crucial to success and compounding healing.
These nutrient-dense additions include:
• Healthy fats (like olive and avocado oils)
• Bone broth
• Organ meats
• Colorful fruits and vegetables
• Fermented foods
• Fish and shellfish
This list includes incredibly nutrient-rich foods that can help fuel deep healing. Overall these
additions represent, ounce-for-ounce, the most nutrient-varied and nutrient-dense foods we
can consume, as well as foods that tend to be anti-inflammatory. You can read more about this
concept in the article The Argument For Nutrient Density.
Autoimmune Wellness © 2024 All Rights Reserved
No unauthorized copying, editing, or distribution 3
Implementation: Transition
During the Transition Phase, each person gets to choose whether they want to move slowly
or quickly towards a fully-compliant elimination phase (either AIP Core or AIP Modified
eliminations).
A slow transition is a gradual, phased approach to eliminating the foods that are initially
avoided on AIP, starting with those foods which are least nutrient dense and most likely to
be driving symptoms. It is much more gentle and often more sustainable, plus a good fit for
those who may experience a lot of overwhelm with such a big dietary change. The downside
is that results take a little longer (although not significantly longer) to realize. The time frame
for doing the eliminations in phases is variable (it can be done over a few weeks or a few
months), but many people find six weeks to be achievable, as used in the AIP medical study
interventions.
In contrast, a quick transition is a fast, sometimes immediate transition to the full elimination
portion of AIP. This transition method might use a three-day quick-start in order to prepare and
is a good fit for those who are desperately ill and/or highly motivated. The downside is that it
is often not sustainable, and a person may burnout before they see results, after realizing that
big dietary changes have a whole life impact.
The reintroduction phase
Whether utilizing the AIP Core or AIP Modified Elimination list, it is important to remember
that entering the reintroduction phase is an important and essential part of the protocol.
During the reintroduction phase, a person progresses through a process of testing their
response to the foods they’ve eliminated, one-at-a-time. The foods are best tested in a specific
order, beginning with foods that are most nutrient-dense and least likely to cause a reaction
and moving toward foods that are least nutrient-dense and most likely to cause a reaction. This
is done in a systematic, staged process that can take a few months when done carefully. This
hard work is rewarded when each person discovers a unique dietary approach that supports
their best health. You can learn more details about this process at the Definitive Guide to
Reintroductions.
Autoimmune Wellness © 2024 All Rights Reserved
No unauthorized copying, editing, or distribution 4
Professional support
If you are still feeling overwhelmed and feel like professional support might be helpful, you
have options! Over 1,000 healthcare providers have been trained in implementing AIP
according to current evidence, including how to customize and personalize depending on each
person’s unique needs.
The AIP Certified Coach practitioner community contains both non-licensed and licensed
providers from across the natural and conventional spectrum of healthcare, located all over
the world, and working in many different languages. You can find health coaches, nutritionists,
fitness professionals, bodyworkers, herbalists, naturopaths, medical doctors, and more.
Search listings to find a practitioner near you on the AIP Certified Coach website.
Looking for more AIP resources?
If you are looking for hard-copy resources for the Autoimmune Protocol, there are plenty.
The Autoimmune Wellness Handbook serves as an all-angles approach to every area
those with chronic illness want to cover, from the Autoimmune Protocol to sleep, stress
management, and connection (and it also contains a library of Core AIP recipes!). The
Autoimmune Paleo Cookbook was the very first AIP cookbook and still a favorite in the AIP
community. The Alternative Autoimmune Cookbook was the first to tackle the emotional
side of healing along with delicious reintroduction recipes. And The Nutrient-Dense Kitchen
contains an impressive library of AIP favorites with an extra focus on accessibility, quick meals,
and nutrient-density.
You don’t need to buy any books to get connected to all the information you need to embark
on AIP, because the mission here at Autoimmune Wellness is to share that information for
free. There are over 100 articles on this site covering every detail of AIP, in addition to over
250 AIP compliant recipes and even more resources and links on our resources page. You can
also tune in to past episodes of The Autoimmune Wellness Podcast for an audio version of the
information presented here.
Autoimmune Wellness © 2024 All Rights Reserved
No unauthorized copying, editing, or distribution 5
