What is AIP?

The Autoimmune Protocol is an elimination and reintroduction protocol that has been specifically designed to help those with autoimmune disease determine their food sensitivities, reverse nutrient deficiencies, balance their gut flora, and heal their bodies.  AIP happens in three phases: the elimination-phase, the maintenance-phase, and the reintroduction-phase.

The elimination-phase involves removing foods that are typically inflammatory in nature and tend to be problematic for people with autoimmune disease, like grains, legumes, dairy, eggs, nuts, seeds, nightshades, and alcohol. If you’d like to learn more about the scientific “why” behind these eliminations, then I invite you to read more on thepaleomom.com.

The maintenance-phase calls for maintaining full elimination for 30-90 days. This time is so important to allow the body time to “reset” and heal. This is often where individuals will start notice a decrease in symptoms and increase in energy and mental clarity. If you’ve been following full-elimination for over 90 days and aren’t seeing much progress, then that is an indicator you might need some deeper troubleshooting and work with a practitioner.

The reintroduction-phase involves the slow and methodical reintroduction of previously eliminated foods. During this phase you’ll basically be conducting a science experiment on yourself to determine your true food sensitivities and create your personalized AIP-template that support long-term health and healing. Check out my post all about reintroducing foods on AIP.

What is Eliminated?

Gluten & Grains

Those with autoimmune disease tend to have a higher rate of intestinal permeability (leaky gut). Gluten and grains are some of the most problematic foods in terms of promoting leaky gut. You can read more about the connection between leaky gut and grains here.

  • Amaranth
  • Barley
  • Buckwheat
  • Bulger
  • Corn
  • Millet
  • Oat
  • Quinoa
  • Rice
  • Rye
  • Sorghum
  • Spelt Wheat


Dairy can be very irritating to the gut lining and trigger allergies, food sensitivities, and inflammation. High quality or fermented dairy may be fine in moderation after the body has had a decent chance to heal. You can read more about this here. 

  • Butter
  • Cheese
  • Cream
  • Ghee
  • Milk
  • Yogurt


Legumes have a similar impact on the gut lining as grains, promoting intestinal permeability and inflammation. You can read more about this impact here.

  • Black Beans
  • Chickpeas
  • Fava Beans
  • Kidney Beans
  • Lentils
  • Lima Beans
  • Peanuts
  • Soybeans


Nightshades can be a big trigger for inflammation and subsequent pain, particularly those with joint problems. Aside from the direct inflammation trigger, nightshades also contribute to damage and inflammation to the gut lining, promoting leaky gut (are you starting to see the connection here?). You can read more about this here. 

  • Tomatoes
  • Tomatillo
  • White potatoes (not sweet potatoes)
  • All peppers
  • Goji Berries
  • Ground cherries (not regular cherries)
  • All nightshade spices
  • Eggplant

Nuts & Seeds

While nuts and seeds can be a rich source of healthy fats, they can be inflammatory to the gut lining due to inhibiting the digestion breakdown process. These are often safely reintroduced once prepared properly. AIP is actually very rich in healthy fats, despite eliminating nuts & seeds, due to the emphasis on quality seafood and animal fats.

  • Almonds
  • Brazil nuts
  • Cashew
  • Chia
  • Canola (including canola oil)
  • Coffee
  • Cocoa/ Chocolate
  • Flax
  • Hemp
  • Hazelnut
  • Pine nuts
  • Pistachio
  • Safflower
  • Sunflower
  • Sesame
  • Walnut
  • Pecan
  • Pumpkin Seeds

Seed & Berry Spices

The logic behind this elimination is similar to that of nuts & seeds. The purpose to temporarily eliminate anything that could possible trigger inflammation to allow the body a chance to heal. These spices are often easily reintroduced after healing has happened.

  • Allspice
  • Anise
  • Caraway
  • Celery Seed
  • Cumin
  • Mustard Seed
  • Nutmeg
  • Cumin
  • Black Pepper
  • Poppy Seeds
  • Fennel Seed

All Alcohol

Alcohol promotes intestinal permeability (leaky gut), thus increasing stress on the immune system and increasing inflammation. It can be enjoyed in moderation after a period of sustained healing. You can read more about why alcohol is eliminated here. 

All Eggs

Eggs are a very common allergen and can really irritate the gut lining. The yolks are often easily reintroduced and can be very nutrient-dense once healing has taken place. You can read more about why eggs are eliminated here. 

All Additives and Refined Sugar

AIP is not a sugar-free diet as natural sugars like honey, maple syrup, and coconut sugar are totally fine in moderation. Food additives like gums, food dyes, and chemicals and highly processed sugars are all inflammatory and just don’t promote healing.

So What is Allowed?

It is important to know that while the AIP emphasizes the removal of these potentially problematic foods, it is centered around the addition of nutrient-dense foods that nourish the body and support healing.

  • All vegetables (a colorful variety of leafy greens, veggies, and starchy root veggies)
  • A lot of seafood
  • Bone Broth
  • Organ Meats
  • Healthy fats (avocado, coconut oil, olive oil, seafood)
  • Meat (best quality possible)
  • Herbs

The Autoimmune Protocol does not promote food limitation for the sake of restriction. The purpose is to temporarily remove foods that could be contributing to inflammation burden and triggering an overactive immune system in those with autoimmunity. The key word here is temporary.  

This is not a prescriptive “diet.” To read more about the difference between a diet and a protocol click here.  The goal of AIP is to find a way of eating that is ultimately tailored specifically to your body’s needs. Think of the Autoimmune Protocol more as a template than a rigid-long term plan. Also, sometimes modifcations to the protocol are necessary during flare ups of Inflammatory Bowel Disease (IBD). Click here to learn more about how to make those modifications.

Autoimmune disease does not appear overnight. While we don’t know the exact cause of autoimmune disease, we do know that there are a myriad of factors spanning a lifetime that contribute to its development. This is why the Autoimmune Protocol also embraces a holistically healthy lifestyle that fosters healing in all facets, not just food. This includes the importance of creating a support network and strong community, prioritizing rest and healthy sleep, managing stress appropriately, incorporating regular movement, and spending time to connect with nature. 

If you’d like to read more check out these two resources:


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.

Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


Copyright and Affiliate Disclosure:

* All recipes, photographs and articles on this site, unless otherwise noted, are my original creations and may not be copied or republished in any form.
The statements made here have not been approved by the Food and Drug Administration. These statements are not intended to diagnose, treat or cure or prevent any disease. You assume full responsibility for how you choose to use this information.
* Amazon Disclosure: “Jesse of AIP Sisterhood is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to [AIP Sisterhood (amazon.com, amazonsupply.com, or myhabit.com)].”

Recent Posts