Almost there! Please complete this form and click the button below to gain instant access.

What Is the Paleo Autoimmune Protocol? 13 Facts About the AIP Diet

What Is the Paleo Autoimmune Protocol? 13 Facts About the AIP Diet

What is the Autoimmune Protocol ? is one of the questions I get asked more often every time I label one of my recipes as compliant for the AIP diet. In this extensive post, I hope I can answer all of your questions on the subject, which happen to be the same questions I had a few years ago when I first learned about the Autoimmune Protocol.

After looking for natural alternatives to improve the autoimmune symptoms I’ve struggled with for years, I finally came across the AIP diet. And since I personally experienced the incredible healing power of the Autoimmune Protocol, I was inspired to tell others and encourage them to give it a try.

In this post you’ll find the an answer to the most common questions I receive about the AIP.

NOTE: The Autoimmune Protocol was started with the recommendations of Loren Cordain and Robb Wolf, who wrote about the autoimmune benefits of following a paleo diet that also avoided eggs and nightshades, and it expanded into a structured protocol compiled by Dr. Sarah Ballantyne Phd, who analyzed the subject scientifically in her book The Paleo Approach.

Make sure to check out their websites too for more information!

13 Facts You Need To Know About the Autoimmune Protocol

1. What Is the Autoimmune Protocol?

The AIP is a protocol designed around a diet and lifestyle program that’s designed to address autoimmune issues (Hashimoto, Chrones, Psoriasis, Rheumatoid Arthritis, Multiple Sclerosis, Lupus, IBS and more) by reducing chronic inflammation, heal the digestive tract and ultimately help reverse autoimmune disease or at least halt its progression.

On the diet front, the Autoimmune Protocol follows a specific version of the Paleo diet with special adaptations. For an initial period called “elimination stage”, you avoid specific inflammatory foods, consume lots of nutrient dense foods and, when your symptoms are lessened or gone, you start the reintroduction process to understand what specific foods trigger an autoimmune response in your body.

However, the Autoimmune Protocol isn’t just about diet. A crucial component of the AIP involves lifestyle factors such as relaxing and reducing stress (practicing self love and meditation are good cures). Getting enough sleep is also crucial (8 to 10 hours of sleep a night are recommended for those with an autoimmune disease). Other lifestyle recommendations on the Autoimmune Protocol are: respecting circadian rhythms (staying out when it’s light and being in the dark at nigh, avoiding blue lights); cultivating social connections; having fun, and exercising moderately on a daily basis.

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Savory Quiche from the AIP Italian Cookbook

2. Why Is Autoimmunity Connected To Gut Health?

80% of our immune system is located in the gut and, without a healthy gut, it’s hard to have a healthy immune system. Dr. Alessio Fasano’s research has shown leaky gut to be one of the preconditions for developing an autoimmune disease (together with genetic predisposition and a specific trigger that the immune system recognizes like a threat).

When the normally tightly knit cells of the intestines are weakened and “leaky”, our gut lining becomes permeable and allows large compounds, such as proteins from food, toxins or bacteria, to enter into our bloodstream.

In order to protect us, our immune system starts making antibodies against them. But because many of these foreign invaders look very similar to our own body’s cells (molecular mimicry), the immune system can get confused and accidentally attack our own tissues.

Which proteins, cells, and tissues are attacked determines the autoimmune disease and its symptoms. In Hashimoto’s thyroiditis, the thyroid gland is attacked. In psoriasis, it’s the cells that make up the skin; in Rheumatoid Arthritis, it’s the joint tissues, and so on.

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet and Leaky Gut
Leaky Gut image from "The Paleo Approach" by Sarah Ballantyne.

3. What Are Some Of The Triggers That Provoke Leaky Gut?

Environmental toxins (such as mercury, pesticides and BPA from plastics), medications (NSAIDS, steroids, antibiotics, birth control pills and acid-reducing drugs), chronic stress (both emotional and physical are associated with the body losing its ability to regulate the inflammatory response), and inflammatory foods, such as dairy, grains, pseudo-grains, nightshades, eggs, sugar, alcohol and GMO’s. Gluten in particular is one of the main culprits for leaky gut, as it triggers the release of zonulin in our intestines, a protein that modulates the permeability of tight junctions between cells of the wall of the digestive tract.

Other causes for leaky gut are candida overgrowth, intestinal parasites, and SIBO (Small Intestine Bacterial Overgrowth), which populates our gut with bad bacteria, fungi and parasites leading to a microbial imbalance in the gut flora called gut dysbiosis.


As you can see from my breath test that measures the Bacterial Overgrowth of the Small Intestine (or SIBO) below, during the course of a year while following the autoimmune protocol I experience a substantial improvement in my gut health.

Ambra's SIBO (Small Intestinal Bacterial Overgrowth) Test Results, November 2015

What is the Autoimmune Protocol?

Ambra's SIBO (Small Intestinal Bacterial Overgrowth) Test Results, November 2016

What is the Autoimmune Protocol?

4. What Are the Gut Healing Foods Recommended On the Autoimmune Protocol?

The AIP Diet focuses a lot on enriching your eating regimen with nutrient dense foods that can repair damaged tissues, modulate the immune system, and heal the gut lining.

Make sure you download my COMPLETE AIP FOOD LIST you find below

In the meantime, here’s  little preview. On the AIP you’ll be nourishing your body with large amounts of leafy and cruciferous vegetables, organ meats (some of the most nutrient dense foods there are), fatty fish and shellfish (rich in vitamin A and D, zinc and various B-vitamins essential for modulating the immune response), bone broth, high quality meats and fats and fermented foods which provide beneficial probiotics.

The Complete AIP Food List for the Autoimmune Protocol

Enter your email and get the COMPLETE AIP FOOD LIST!

5. What Are the Foods To Eliminate During the AIP Diet?

Here above you can download an exhaustive AIP FOOD LIST that includes all the foods you should avoid while you’re on the Autoimmune Protocol.

In general, while on a standard paleo diet you are suggested to avoid all grains (even the gluten free ones), dairy, legumes, industrial seed oils, alcohol and sugar, the Autoimmune Protocol requires you to step forward and also avoid eggs, nightshades (e.g. potatoes, tomatoes, eggplant, peppers), coffee, chocolate, nuts and seeds during the initial elimination phase.

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Savory Quiche from the AIP Italian Cookbook

6. How Long Is the Elimination Phase of the AIP Diet?

While some people start seeing improvements in their symptoms after the first 30 days, many people need to follow a strict AIP diet for at least two to three months (or more, depending on their level of inflammation) before they are ready to reintroduce foods. Once you are ready to reintroduce, you’ll follow a step-by-step process that will allow you to scout foods that are triggering an autoimmune response and create a personalized healing diet that’s healthy for you.


Personally, I did two cycles of AIP elimination: the first lasted four months and the second one lasted six. Only after completing the second cycle correctly and following the reintroduction phase step-by-step, I was able to find a lasting and personalized eating regimen that was good for me.

7. How Important Is It To Be Strict During the Elimination Phase of the AIP?

Every time you eat inflammatory foods, your body will produce antibodies that can ignite an attack on your immune system for days, weeks and even months. Cheating means that you have to start your reset all over. That’s why committing 100% to avoiding certain foods during the elimination phase is crucial to see improvements and get to that symptom-free (or lessened symptoms) stage that you need to achieve before you start reintroducing.


I have never cheated once during my two cycles of AIP elimination stage. As you can imagine, committing to the AIP is not exactly a breeze, and after you know the setbacks that cheating can induce, you definitely feel like you need to stay on track and not compromise all the work and efforts you’ve put in so far.

To cope with cravings, I have challenged my creativity in the kitchen and developed recipes that could recreate the dishes I missed the most in an AIP compliant way. This is how my “AIP Italian Cookbook” was born.

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Spaghetti with Meatballs from "The AIP Italian Cookbook"

8. How Does the Reintroduction Phase Work?

The second question I get asked the most after What Is The Autoimmune Protocol ? is How and When Can I Reintroduce Foods? Please check out this extensive post I wrote about reintroducing foods on the AIP. Not only did I write it while I was facing the reintro phase myself, but I also interviewed two major experts in the autoimmune wellness field: Mickey Trescott and Angie Alt.

9. What Results Can I Expect From the AIP?

While there are many success stories of people (including myself) who achieved remission of their autoimmune symptoms, it’s important to acknowledge that the AIP is not a cure, but a lifestyle that, if followed religiously, allows you to keep inflammation under control. Depending on the stage and gravity of your autoimmune disease, you might still need to match the AIP with further support from medication or a personalized supplement plan.

That being said, if you can remove the foods and toxins that are stimulating an autoimmune response in your body and nourish it with nutrients, you can help the healing process, significantly reduce symptoms and even put the disease into remission.

10. Can I Take Care Of My Autoimmune Disease On My Own If I Follow The AIP?

I strongly recommend that you work with a functional medicine practitioner to have all your lab tests done and develop a comprehensive health recovery plan that includes dietary changes, supplements, stress management techniques and other lifestyle changes.


It’s not easy to find a person you really trust and that is competent enough to guide you through this alternative healing process. I had to go through to three bad experiences before I finally found a functional medicine doctor that’s perfect for me.

Don’t give up and continue your search until you are fully satisfied. I used the Functional Medicine Practitioner Directory to find a doctor that worked in my ar

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Italian Spiedini from the AIP Italian Cookbook
What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet

11. Can I Simply Test for Food Allergies Instead of Going Through an Elimination Diet?

Unlike food allergies, food intolerances have a milder outcome, but their cumulative effect can provoke inflammation in the body and stimulate the immune system. Especially in those individuals who already suffer from an autoimmune disease, food intolerances can exacerbate symptoms and worsen their conditions.

Unfortunately, the tests we have today to identify food intolerances aren’t very accurate and they give a lot of false positives and false negatives.

Only an elimination diet (just like the initial phase of the AIP) is a good way to diagnose food intolerances. When you see clear improvements in your autoimmune symptoms and the healing process has begun, you can start to reintroduce foods one at a time and verify if you can tolerate them or not.

12. Can I try the AIP If I Don’t Have an Autoimmune Disease?

This is a really personal matter as every body is different and thrives on different foods. There are many people with chronic pain or autoimmunity who will do just fine following a healthy gluten, sugar and dairy free diet. While only 1% of the population has Celiac disease, it’s estimated that one in 30 people have Non Celiac Gluten Sensitivity, meaning that eating gluten provokes and inflammatory reaction in their body. Furthermore, 99% of these people are undiagnosed and keep putting inflammatory foods into their bodies without even knowing it.

Some other people can thrive and see improvements on a Paleo nutrient dense diet (avoiding grains, dairy, legumes, industrial seed oils, alcohol and sugar). The people who don’t see satisfying results from these two diets can opt to spend some time on the AIP to restore their gut lining and lower inflammation before being ready to reintroduce other foods.

Many people who suffer from chronic pain suffer have undiagnosed autoimmune diseases and the AIP can be very helpful in determining the


When I first learned about my Non Celiac Gluten Sensitivity and dairy intolerance in 2013, I started off combining a gluten and dairy free diet with a vegan regimen. Unfortunately, that type of diet was not good for me and it took me a long time to accept that, as I really wanted to eat that way. When my functional medicine doctor convinced me to try a paleo diet and I started reaping the first benefits of it (especially visible on my skin and stomach bloating), I was finally ready to give the Autoimmune Protocol a try and the results were wonderful.

After 2 cycles of strict AIP diet, I managed to reintroduce many of foods I couldn’t tolerate before, from rice to chickpeas.

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Pizza with Tomato Free Marinara Sauce from "The AIP Italian Cookbook"
What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Grain Free Oatmeal Porridge from "The AIP Italian Cookbook"

13. I’ve Tried the AIP for 30 Days Already but Still Haven’t Seen Any Improvements

Assuming that you are doing the AIP right (managing stress, focusing on nutrient dense foods, getting in your offal and bone broth, maintaining a positive mindset and committing 100% to the process) the AIP can take time!

First of all, it takes a long time to heal your gut and allow your immune system to calm down. Also, autoimmune diseases and inflammation aren’t only related to diet. Other factors can come into play, such as gut infections like SIBO (see Question N. 3), gut dysbiosis, toxin overload, parasites etc.


It took me over 2 years to get to a point in which I was satisfied about the results I obtained. Like I mentioned before, I went through the Elimination Phase the AIP twice: the first time for 4 months and the second one for 6 months. And I had to deal with all of the issues (yes, ALL of them) listed above before my body was ready to heal.

Be patient and trust the process. It will happen. Maybe just not in 30 days 😉

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet
AIP Cannoli from "The AIP Italian Cookbook"

I hope you enjoyed this post and that I answered to all of your questions related to what is the Autoimmune Protocol.

Make sure you share this article with somebody who’s affected by chronic pain, leaky gut problems or autoimmune issues so that they can look into a powerful natural alternative to better manage their symptoms and live a healthier life!

Love,   Ambra

The Complete AIP Food List for the Autoimmune Protocol

Enter your email and discover what FOODS are allowed on the Paleo Autoimmune Diet!

What Is the Paleo Autoimmune Protocol? 10 Things You Need To Know About the AIP Diet

You May Also Like

Leave a Reply