Your Definitive Guide To The Autoimmune Protocol (AIP Diet) + How It Can Help Manage Your Symptoms


The Autoimmune Protocol diet, or the AIP diet for short, is a diet designed to help lower inflammation and alleviate symptoms in those diagnosed with autoimmune diseases.

In my functional medicine clinic, I often use the AIP diet as a baseline for many of my patients who come to me with autoimmunity and have found it extremely beneficial at helping them find relief from symptoms they have been struggling with for years.


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How the AIP diet works

In order to understand how the AIP diet works, we first need to understand autoimmunity.

In autoimmune conditions, it is believed that a genetic weakness is triggered by an immune response to toxins such as food proteins leaking into the bloodstream through a compromised gut lining or chronic viral, bacterial, yeast, or parasite infections. 

All of these involve out-of-control inflammation which is an immune system trigger. This inflammatory-immune response can both cause and increase intestinal permeability - also known as leaky gut syndrome - further perpetuating the inflammatory-immune cycle.

Since certain foods can contribute to gut permeability and drive-up inflammation in some people, the AIP diet aims to remove all of these foods in favor of nutrient-dense food sources that promote gut health.

Typically, the autoimmune protocol diet happens in two phases - the elimination phase and the reintroduction phase.

Phase 1: Elimination

This phase is the core of the AIP diet. This is when you take out all of the potentially triggering foods and focus on the nutrient-dense foods you can eat on the list of allowed foods.

Phase 2: Reintroduction

After a set time period of eating only the AIP diet allowed foods, you can then reintroduce certain foods - starting with the least likely to trigger inflammation to the most likely - in order to see what your body can handle and what it can’t.

The goal of these two phases of the AIP diet is to give your body time to heal before reintroducing foods to see what foods trigger inflammation and which foods don’t, so you know what flares up your autoimmune symptoms. The reintroduction phase is going to look different for each individual since everyone’s body reacts differently to different foods.

How the food helps and affects the body

The AIP diet is just as much about the foods you do eat as it is about the foods you don’t eat. For example, if you aren’t actively fueling your gut with foods that can heal it, inflammation and gut permeability will still remain even after a prolonged period of eliminating certain foods.

Is AIP and paleo the same?

The AIP diet and paleo diet are similar when you look at the allowed foods. Both diets put a major focus on eating clean, whole food sources that are minimally - if at all - processed. The biggest difference between the AIP diet and the paleo diet is that the autoimmune protocol eliminates a lot more foods that tend to be more inflammatory and irritating to the gut in those with autoimmune conditions.

AIP Diet Foods you should eat

Animal protein: all types of beef, poultry, and game

Seafood/shellfish: all types of seafood and shellfish are fair game to enjoy.

Vegetables: any and all vegetables - raw or cooked - with the exception of nightshades (listed below)

Fruit: any and all fruit - with the exception of nightshades (listed below) - in moderation

Natural sweeteners: dates, 100% fruit juice, pure maple syrup, raw honey - in moderation

Oils: Avocado oil, coconut oil, olive oil

Grain-free flours: almond, coconut, cassava

Herbs and spices: with the exception of nightshades (listed below)


Bone broth

Dairy alternatives: ghee, coconut milk

Food you should avoid on the AIP diet

Legumes: Peanuts, black beans, chickpeas, kidney beans, lentils, soy, and soy-based products

Due to their lectin and phytate content they can be difficult to digest and are hard on your gut while it is trying to heal.

Nuts and seeds: chia seeds, hemp seeds, walnuts, almonds, cashews, etc. along with nut-based butters, flours, and oils

These are often coated in inflammatory oils that flare-up autoimmune symptoms and can be difficult to digest.

Eggs: Even though eggs are super nutrient-dense with 6g of protein and 5g of fat, egg whites contain a compound called albumin that can cause reactions for people with autoimmune conditions.

Dairy: cheese, yogurt, ice cream, milk, butter, cream, and any other product containing cow or sheep’s milk

Nightshades: white potatoes, tomatoes, peppers, eggplant, goji berries, okra, tomatillos, paprika, cayenne pepper, ashwagandha

This group of botanical plants contains compounds known as alkaloids that can contribute to inflammation and symptom flare-ups in those struggling with autoimmune conditions. 

Gluten: wheat, barley, rye, and any products made from these ingredients including flour, bread, and pasta

Gluten-free grains: rice, quinoa, oats, sorghum, buckwheat, corn

Since the protein in these grains is so similar to gluten, an overactive immune system may mistake them for gluten and begin an attack.

Sugar and artificial sweeteners: cane sugar, sugar in the raw, turbinado, corn syrup, aspartame, stevia, monk fruit, brown rice syrup, and any products with the addition of these sweeteners

Inflammatory oils: vegetable, canola, corn, soybean, safflower, rice bran, and grapeseed




How long should you do the AIP diet?

How long you should do the AIP diet depends on your individual health case. There is no one-size-fits-all when it comes to your health. Since your biochemistry is different from anyone else’s, how you respond to a particular diet is going to differ even if you have the same diagnosis.

On average, the AIP diet should last a minimum of 90 days before you can start reintroducing certain foods back into your diet. However, if you are more sensitive it may take longer to reintroduce foods back into your diet depending on your level of gut permeability and inflammation.

How can you tell it is working?

You can tell the AIP diet is working by a reduction in symptoms. Although autoimmune conditions never completely disappear, you can put symptoms into remission and minimize flare-ups by focusing on healing your gut and driving down inflammation with an autoimmune diet protocol.

You also have to remember that healing takes time. You should notice an improvement in symptoms of some sort after a couple weeks, with more and more improvements the longer you follow the AIP diet as you work toward long-term, sustainable healing.

Applying the AIP diet responsibly

Other factors to consider

When looking at the AIP diet, we also have to take into account bio-individuality - the concept that everyone’s biochemistry is completely different even if diagnosis are the same.

Some people have specific food allergies/sensitivities, take certain medications, or have a higher level of physical activity that needs to be considered while on the AIP diet.

You still have to look at these factors and tailor the AIP diet to fit within each person’s particular parameters. 

Functional medicine understands the importance of bio-individuality, and works to leverage the AIP diet to fit your individual health needs and goals - not forcing the AIP diet to work for you.

Taking a holistic approach to autoimmune health

In functional medicine, we realize that there is more to health than diet alone. We aim to look at the entirety of your health case and consider other factors that play a role in your inflammation levels and autoimmune condition such as:

Sometimes, it takes certain lifestyle changes to target these other triggers in addition to an AIP diet for a well-rounded, holistic approach to healing. 

With over a decade of specializing in autoimmune conditions, it is my job to get to the root cause of why you feel the way that you do. By uncovering underlying issues and customizing a plan to lower inflammation in conjunction with dietary changes like the AIP diet, you can be on your way to a life free from autoimmune flare-ups.

Ready to take the next step? Take The Inflammation Spectrum Quiz to discover where you are on the spectrum.


Thinking of starting the AIP diet? We can help! As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.


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  1. Fasano, Alessio. “Zonulin, regulation of tight junctions, and autoimmune diseases.” Annals of the New York Academy of Sciences vol. 1258,1 (2012): 25-33. doi:10.1111/j.1749-6632.2012.06538.x

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Evidence-based reviewed article

Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum, and Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

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Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel