GAPS Intro Diet Modified for Autoimmune Disease

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GAPS Intro Diet Modified for Autoimmune Disease | Phoenix Helix

“In science the important thing is to modify and change one’s ideas as science advances.”
~ Herbert Spencer

The Origin of This Post

If you’ve followed my blog for a while, you know that I started with the GAPS diet, and then transitioned to the Paleo Autoimmune Protocol (AIP), because I was still struggling with inflammation and autoimmune flares. Katy Haldiman had the same experience, and we’re not alone. Many people with autoimmune disease struggle on the GAPS protocol because it reintroduces foods very quickly, that are common food intolerances for people with autoimmune disease (such as nuts, dairy and eggs.) The GAPS protocol uses a skin sensitivity method to determine food intolerance. Unfortunately, this doesn’t work for many of us.

Katy is a nutritional therapist whom I interviewed on a recent episode of the Phoenix Helix podcast. This topic came up, and she mentioned that she modified the GAPS Introduction Diet to use with her autoimmune clients, with great success. I asked her if she’d share it with us, and she agreed. Here’s Katy, writing about this protocol:

Katy’s Consultation Method

In the ancestral health community, there are several healing diets for those struggling with autoimmunity and chronic health issues, including the Paleo Autoimmune Protocol (AIP), the Wahls Diet, the Specific Carbohydrate Diet, and the GAPS Diet. All of these diets share certain similarities, as well as key differences. As a nutritional therapist, my role is to formulate a customized nutritional template that (1) addresses the client’s bioindividual needs and (2) facilitates the discovery of food and environmental triggers that contribute to symptoms. I often draw upon key principles from a combination of these various healing diets when I structure nutrition and lifestyle recommendations for a client. For clients that are struggling with moderate to severe digestive symptoms or are immunocompromised, I often begin by recommending a modified version of the GAPS Introduction Diet.

A Brief Overview of GAPS

Developed by Natasha Campbell-McBride, MD, the GAPS protocol consists of three components:

  1. Therapeutic Diet
  2. Supplementation
  3. Detoxification and Lifestyle Changes

The dietary component of GAPS builds upon the Specific Carbohydrate Diet, with an additional emphasis on healing broths and fermented foods. The GAPS Diet has a 6 stage Introduction Diet (which typically lasts 3-4 weeks) followed by the Full GAPS Diet (which is recommended to be followed for 18 months- 2 years). The GAPS Introduction Diet can be thought of as a “gut reset” and it is designed to remove inflammatory food triggers, heal the lining of the digestive track, and set the stage to restore bio-diverse gut flora. The Full GAPS Diet is similar to the Paleo Diet, except that it includes some dairy and legumes.

Why Are Modifications Necessary?

While the GAPS Diet as outlined by Dr. Campbell-McBride has helped countless people to heal their guts, there are some foods permitted in the introduction stages that I have found to be problematic for many clients struggling with digestive and/or autoimmune symptoms. These foods include:

  • Dairy (introduced as fermented dairy in stage 1, ghee in stage 2, and butter in stage 4)
  • Eggs (introduced in stage 2)
  • Nuts (introduced as nut butter in stage 3 and nut flour in stage 4)
  • Nightshades (introduced in stage 5)
  • I modify the GAPS Introduction Diet by eliminating these foods while progressing through each of the stages.

Why Do the Introduction Diet at All? Why Not Simply Jump to the AIP?

Many people can go straight to the AIP and do well. In my practice, I recommend the Modified GAPS Introduction Diet for clients that have gastrointestinal diseases, such as Crohn’s disease, ulcerative colitis, and irritable bowel disease or persistent digestive symptoms, such as reflux, diarrhea, bloating, abdominal pain, or constipation. I may also recommend it for clients with autoimmune disease that have attempted other healing diets, but have not been able to control their symptoms as well as they would like. The GAPS Introduction diet gives the digestive system time to rest and recover. If you don’t fall into these special categories, you may never have a need to do GAPS Intro.

My modifications to the GAPS Introduction Diet are in line with the dietary recommendations of the AIP. However, the protocol still varies from AIP in the preparation of foods (cooked foods only during the first few introductory stages) and the step-wise progression that foods are reintroduced in each stage. After the client progresses through the modified GAPS Intro stages, I may recommend transitioning to the AIP or another healing diet depending on the client’s needs. It’s important to keep in mind that the GAPS Introductory Diet is only designed to be followed for a limited period of time.

Another modification that I make to the GAPS introduction Diet concerns the amount of non-dairy fermented foods. Fermented foods can be healing, but only a small amount is generally necessary in order to reap their benefits. It is possible to consume too many fermented foods, which can exacerbate digestive symptoms. The main benefits of fermented foods are in the nutrients produced when the bacteria ferment, including B vitamins, enzymes, and bioavailable flavonoids. The probiotics present in fermented foods do not actually colonize the gut and cannot significantly alter gut dysbiosis. While fermented foods are generally beneficial to digestive health, it is wise to moderate the amount consumed and consider additional supplementation with a high quality probiotic that has the ability to colonize the gut, like Megaspore. *Editorial update by Eileen: I’ve been interviewing a number of healthcare professionals on my podcast recently, and the opinion on fermented foods vs. probiotics varies greatly. Some like Katy believe that probiotic supplements are an essential part of a healing protocol. Others believe they can actually be healing stumbling blocks. Why the difference? Because probiotics are immune system stimulants. For people with autoimmune disease, this can go one of two ways: (1) They can help rebalance your immune system in a healthier direction. (2) They can cause an autoimmune flare. Always start slow with both probiotics and fermented foods, tuning into your body and only increasing the amount if well tolerated. Don’t take any probiotic that makes your symptoms worse. It often takes some trial and error to find one that works well for you.

Katy’s Modified GAPS Introduction Diet


  • GAPS: Soups made with homemade stock, meat/fish, and non-fibrous vegetables. Add a small amount of fermented dairy or fermented vegetable juice to the soup. Ginger honey tea and broth between meals.
  • AIP Modifications: Avoid dairy, choosing fermented vegetable juice instead.


  • GAPS: Continue with soups, but you can also eat casseroles and stews. Avoid spices, and use sea salt and herbs instead. Add raw organic egg yolks and soft-boiled eggs to the soups. Start cooking with ghee. Add fermented fish to the diet.
  • AIP Modifications: Avoid eggs and ghee. Watch your response to fermented foods carefully, and only increase as tolerated.


  • GAPS: Continue with foods from earlier stages. Add mashed avocado to the soups. You can expand egg consumption to include scrambled eggs. And you can now eat pancakes made with nut butter, eggs and squash. Continue to increase fermented foods, adding fermented vegetables to the diet.
  • AIP Modifications: Continue to avoid eggs and dairy. Avoid the pancakes, due to the nuts. Eat fermented foods as tolerated, but limit to reasonable quantities.


  • GAPS: Continue with foods from earlier stages, and add roasted and grilled meats, (not overcooked). Add extra virgin olive oil to each meal. Add freshly pressed juices beginning with carrot juice. You can now have bread made with nut flour, butter and eggs.
  • AIP Modifications: Continue to avoid eggs, dairy and nuts, which means avoiding the bread.


  • GAPS: Continue with foods from earlier stages, and add raw vegetables to the diet, including tomatoes. Add some fruit to your freshly pressed juices, but avoid citrus. You can now eat peeled and cooked apples.
  • AIP Modifications: Continue to avoid eggs, dairy and nuts. Avoid nightshade vegetables.


  • GAPS: Continue with foods from earlier stages, and add raw fruit, beginning with peeled apple. You can now bake desserts, using dried fruit as the sweetener.
  • AIP Modifications: Continue to avoid eggs, dairy, nuts and nightshades.



GAPS Intro Diet Modified for Autoimmune Disease | Phoenix HelixKaty Haldiman, MS, RN is a registered nurse, nutritional therapist, and personal trainer. Update 2020: Katy has retired her nutritional therapy practice and is currently nursing full-time.

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