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 or Prescript Assist. *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 experts in the field warn against the use of probiotics for people with autoimmune disease, because they can stimulate an already overactive immune system. Others say that the microbiome is unique to each individual and mass-produced probiotics aren’t a good idea. I recommend n=1 (self-experimenting). Only take probiotics if they improve your symptoms and avoid any that make your symptoms worse. If you do well with fermented foods and eat a wide variety of vegetables that naturally feed a healthy microbiome, there may be no benefit to probiotic supplementation.

Katy’s Modified GAPS Introduction Diet

Stage 1: 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. Avoid dairy, choosing fermented vegetable juice instead.
Stage 2: 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. Avoid eggs and ghee. Watch your response to fermented foods carefully, and only increase as tolerated.
Stage 3: 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. Continue to avoid eggs and dairy. Avoid the pancakes, due to the nuts. Eat fermented foods as tolerated, but limit to reasonable quantities.
Stage 4: 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. Continue to avoid eggs, dairy and nuts, which means avoiding the bread.
Stage 5: 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. Continue to avoid eggs, dairy and nuts. Avoid nightshade vegetables.
Stage 6: 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. Continue to avoid eggs, dairy, nuts and nightshades.
Transition: to the Full GAPS Diet. Transition to either the AIP or the Wahls Protocol.


For complete information on the GAPS protocol, read Gut and Psychology Syndrome by Dr. Natasha Campbell-Mcbride. For complete information on the AIP, read The Paleo Approach by Dr. Sarah Ballantyne.

GAPS Intro Diet Modified for Autoimmune Disease | Phoenix HelixKaty Haldiman, MS, RN is a registered nurse, nutritional therapist, and personal trainer. After several years of practicing in the conventional health care system, Katy discovered the Paleo lifestyle as a way of eliminating symptoms of her own gastrointestinal and autoimmune disease. Now, Katy’s mission is to help others make healing changes in their own lives through the power of real food and other ancestral health techniques. Katy is co-creator of Paleocare: The Nurses’ Guide to Real Food and co-host of the Paleocare Podcast. She consults with clients all over the world via Skype and telephone. You can find Katy at The Paleo Nurse.

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24 thoughts on “GAPS Intro Diet Modified for Autoimmune Disease

  1. Pingback: GAPS Intro Diet Modified for Autoimmune Disease | Paleo Digest

  2. Thanks – this was really helpful. I have ulcerative colitis and, after spending time researching the different options, opted to follow a paleo and then the AIP. However, I had to modify it quite considerably in the early stages, e.g. to cut out uncooked veg/fruit and certain high FODMAP foods which my body struggled to digest. It is working well for me at the moment, but it’s helpful to have this as an option should I get another flare-up of the disease.

    • Thanks for sharing your experience, Emma! It sounds like you came up with a similar modification for yourself. You’re very wise. While hopefully you are past the flare stage yourself, I think this diet would be perfect for anyone navigating a UC flare.

  3. Eileen, this is just what I was going to try to create for myself, so I am excited to have the professional guidance from Katy. I am taking part in the SAD to AIP program right now and know that I will need to further limit my diet in order to treat my rheumatoid arthritis (RA) and several toxic intestinal over-growths (confirmed by lab tests). Like you, GAPS worked for me, but I reintroduced too quickly, then cheated now and then, causing me to begin to relapse back into my peripheral neuropathy (PN). That’s when I found you and can now move forward again. Yeah!

  4. Do you know if this would work for someone with histamine intolerance? The low histamine diet says no cultured foods. Thanks!

    • Hi Amber. I wouldn’t recommend this for anyone with histamine intolerance, not so much for the fermented foods (because Katy recommends such a small amount). Rather, because of the high use of broth, which is a high-histamine food. If you’re looking for AIP + Low-Histamine recipes, check out Grazed and Enthused. Also, 1/2 the recipes in the new AIP Breakfast Cookbook are either low-histamine as written or easily modified (a chart is located at the end of the cookbook.)

  5. “The probiotics present in fermented foods do not actually colonize the gut and cannot significantly alter gut dysbiosis.”

    I’m confused. I thought the microbes in fermented foods DO colonize the gut – which is part of the reason to eat them! Suddenly you are telling us this is not true (and recommending a brand of probiotic only sold to “health professionals”. hmmmm…) Can anyone out there clear up this confusion? Are fermented foods good for getting the “good” microbes into our guts? Or are we deluded into thinking eating a food can/should do the job of a specialty formula?

    • The first time I learned that fermented foods don’t colonize the gut, I was equally shocked and confused, and wondering why I was eating them, so I totally understand your feeling! Sarah Ballantyne writes about this in The Paleo Approach. Fermented foods are medicinal on their way through our bodies. They have anti-inflammatory effects, they tighten the junctions of our gut lining (helping to heal leaky gut), and they help us digest our food. So, they’re very beneficial, but they don’t stick around. That’s why we eat them every day. The probiotics that are shown to “stick around” are spore-based ones, like the brand Katy mentioned, and another one which you can buy yourself: Prescript Assist.

      However, if you’re someone who wants to try food first, resistant starch has been shown to increase the beneficial bacteria in our gut in a colonizing fashion. Green plantains are an AIP-friendly source of resistant starch. However, that’s contraindicated (not allowed) during the GAPS Introduction diet, because starch and fiber are removed from the Intro Diet. (Unfortunately resistant starch can also feed pathogenic bacteria, so the GAPS Introduction diet is designed to starve out bacteria overall – temporarily – and set “a clean slate” for colonizing with the good guys.) That’s why Katy recommended a GAPS-friendly solution “in a bottle” for anyone following the GAPS Intro Diet.

  6. thanks! now I understand. I am not following the GAPS plan, but I bought some probiotic capsules. I love my homemade sauerkraut too, so its all good!

  7. I had food sensitivity tests done and they came back positive for some foods. Do I also need to avoid/remove these foods during the GAPS intro or AIP? Then do I add one back in at a time? Thanks for all your help!

    • Hi Marcie. I think that’s far too many restrictions. Food sensitivity testing is notoriously inaccurate. Dr. McBride actually talks about this in her book. When you have leaky gut, your immune system reacts, and if you got tested every day, your results would be different every day, based on what you’ve been eating. That’s not a true sensitivity. That’s just a sign that your gut needs healing. So, I recommend setting aside your test results and simply doing GAPS Intro. Modified for AIP. If you need further guidance, Katy is available for 1:1 consults.

  8. Also, you mentioned Katy recommends a GAPS friendly “solution in a bottle”. What is that? Did you all post it somewhere or is it on her pod cast. I am desperate to help my 6 month old little boy, with severe eczema, belly issues and not having consistent bowel movements. He also cries and is uncomfortable most of the time. It is heartbreaking!

    • Hi Marcie. Katy recommends the Megaspore brand of probiotic, but it’s only available when prescribed by a practitioner like Katy: you would need to be working with her to have access to it. I’m also not sure it would be suitable for infants. There are supplements like GutPro Infant designed for infants, but before giving your baby any supplements, I would definitely recommend talking with someone with more expertise than me. Gentle hugs to you. Your love shines through!

  9. Marcie, if you are breastfeeding, you can take the probiotics. I dont know if they will transfer to your milk, but it will help your digestion.
    Are you doing AIP?

  10. Thanks for all the information! I have a leaky gut due to taking antibiotics about 3 months ago, but not an autoimmune disease. I am extremely sensitive to gluten and all grains, especially corn. I have severe hives that will not go away with the regular Paleo diet, but no other symptoms. Would this diet be good for me?

  11. I never comment on sites/blogs but I have to say THANK YOU! This is EXACTLY what I’ve been looking for because I have serious gut issues along with Celiac and Lyme disease. I’ve been on GAPS Intro Stage 1 for a while and while it was hard without carbs, my gut stopped hurting for the first time in years and my stool was normal! But when I added the fermented dairy in stage two, I got SERIOUS inflammation including cystic acne! So I cut out dairy again (which I have been off of since I got Lyme disease) and then wondered how I was going to keep going on GAPS when there is SO much dairy! THANK YOU! My nutritionist wanted me to go AIP and I did for a couple of months before GAPS and it helped a lot and my skin completely cleared up and my energy was higher than ever but when I introduced nuts I got SO sick and was in so much pain intestinally I couldn’t work or do anything. So I got scared and stopped AIP and went to GAPS. Thanks for making the way easier.

  12. Good morning Eileen, I just discovered your Phoenix Helix our site. I am glad you share such wonderful information. I was wondering if you could please let me know your thought on DE. I just started Diatomaceous about a week ago. 1 Tablespoon in the morning. I have suferred with severe stomach issues from Autoimmune Disease. I am a vegetarian except for eggs and grass fed gelatin. I try to follow the AIP diet. Is DE as good as the claims are?

    • Hi Victoria. I have no experience with DE, but I’m skeptical of any supplement with wild claims. I believe in food first. Wishing you wellness!

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