What is Autoimmune Paleo or AIP Diet?

The Autoimmune Protocol is a diet that helps heal the immune system and gut mucosa. It is applicable to any inflammatory disease.

We have a problem in this country with how we eat, treat disease and heal disease. AIP addresses inflammation in the gut that causes Autoimmune Disease. Autoimmune disease is a condition where the body cannot tell the difference between healthy tissue and foreign invaders and a hypersensitive reaction occurs. The body starts self-tissue attack. For months or perhaps years, this self-tissue attack can occur silently until full blown autoimmune disease develops. There are more than 80 types of "official" autoimmune disorders (and MANY more being discovered daily) but all autoimmune disease have in common is tissue self-attacking in places like the thyroid gland, brain tissue or salivary glands, to name a few.

The Autoimmune Protocol (AIP) diet works to reduce inflammation in the intestines. Many elimination diets are not complete enough and often do not remove immune triggers that promote inflammation in the gut. AIP works to calm inflammation in the gut and also calm inflammation in the body. And while autoimmune disease can never be cured, it can be put into remission. The AIP diet is geared toward healing the intestinal mucosa and supporting low inflammation in the body that can temper the fires of an autoimmune flare-up. First I would like to say that this is our interpretation. There is more than one interpretation of how to “follow” the Autoimmune Protocol (AIP) diet. I call it a lifestyle because in a modified form it is how I eat and live my life. It is also how I recommend my autoimmune clients to eat in their own modified form long term as well.

The Autoimmune protocol has been said to be a version of the Paleo diet, but really, I see that it is so much more than that; it is a dramatic way to address inflammation that is driving Autoimmune Disease that has its beginning roots in the gut. Diet is one aspect of healing. And, although it is the largest aspect of long term health, in the short-term, there are other components that require the help of a skilled practitioner. I suggest you find one that is trained. I personally have a professional practice primarily around helping those on this diet as well as nutritional lab work evaluations, supplement protocols and dietary support. Please email me at info@aiplifestyle.com if you would like to set up an appointment and work together remotely. There are many divergent paths that have an overlap with the AIP lifestyle like Autoimmune disease, adrenal fatigue, H-P Axis imbalances, parasites, SIBO, liver congestion, hormone imbalances, insulin resistance that play a role in how you may use supplements along with the AIP diet to heal your body. Generally, I suggest a 6-8 week protocol with no cheating. When I say “no cheating”, I say this with a “pretty please”. This diet counts on you to put your effort into it, and unfortunately the nature of high allergen foods is such that even small amounts of slip-ups can set you back significantly. Each person who decides to try the AIP diet should work with their practitioner to determine if they are candidates for a low histamine, low latex and/or low FODMAP in addition to following AIP. This is where you will benefit from having an experienced, clinically seasoned practitioner to help personalize your AIP plan. Other adjunct protocols may include: functional blood chemistry, saliva hormone testing, saliva adrenal testing, stool testing and antibody tests. 

I share this all with you as an expert AIP Nutritionist. I am an authority in the AIP movement. I always recommend working with an experienced practitioner when starting AIP and getting blood work and other functional tests like adrenal/cortisol and hormone saliva tests. If you have dysglycemia, insulin resistance, anemia (not all anemias are from low iron!), intestinal or other infections like h. pylori, SIBO, h-p axis issues, adrenal dysfunction, you may not get better on the AIP diet alone. I see this quite a bit in my nutrition practice.  If you have been on the AIP diet and are not seeing results you wanted, or are looking for a heart-centered approach to autoimmune disease please contact me directly for information on how to set up an appointment with me. I primarily use Skype for both my AIP clients and The Loving Diet Program. For more information about me and working together, go to this page. 

Phase 1

6-8 Weeks

Not Allowed:

  • Nuts (including nut oils like walnut and sesame seed oils)
  • Seeds (including flax, chia, pumpkin, sunflower, sesame and culinary herb seeds like cumin and coriander)
  • Beans/Legumes (this includes all beans like kidney, pinto, black as well as Soy in all its forms)
  • Grains (Corn, Wheat, Millet, Buckwheat, Rice, Sorghum, Amaranth, Rye, Spelt, Teff, Kamut, Oats etc)
  • Alternative sweeteners like xylitol, stevia, mannitol
  • Dried fruits and/or over-consumption of fructose (I recommend up to 2 pieces of fruit a day)
  • Dairy Products
  • All Processed Foods
  • Alcohol
  • Chocolate
  • Eggs
  • Gums  (guar gum, Tara gum, Gellan gum, Gum Arabic)
  • Nightshades (tomatoes, potatoes, peppers, eggplant, paprika, mustard seeds, all chili's including spices)
  • No vegetable oils (NOTE: olive oil, lard, palm oil, cultured grass fed ghee and coconut oils are permitted)
  • Culinary herbs from seeds (mustard, cumin, coriander, fennel, cardamom, fenugreek, caraway, nutmeg, dill seed)
  • Tapicoa. I eliminate this the first 6-8 weeks because it is a known gluten cross reactor according to Cyrex Labs Gluten Cross-Reactivity Test


  • Vegetables (except nightshades)
  • Fruits (limit to 15-20 grams fructose/day)
  • Coconut products including coconut oil, manna, creamed coconut, coconut aminos, canned coconut milk (with no additives like guar gum and carageen or bpa lined cans) shredded coconut (this list does not include coconut sugar and nectar)
  • Fats: olive oil, coconut oil, avocados, lard, bacon fat, cultured ghee (certified to be free of casein and lactose)
  • Fermented Foods (coconut yogurt, kombucha, water and coconut kefir, fermented vegetables)
  • Bone Broth
  • Grass Fed Meats, Poultry and Seafood
  • Non-Seed Herbal Teas
  • Green Tea
  • Vinegars: Apple Cider Vinegar, Coconut vinegar, red wine vinegar, balsamic (that has no added sugar)
  • Sweeteners: occasional and sparse use of honey and maple syrup (1 tsp/day)
  • Herbs: all fresh and non-seed herbs are allowed (basil tarragon, thyme, mint, oregano, rosemary, ginger, turmeric, cinnamon, savory, edible flowers)
  • Binders: Grass Fed Gelatin and Arrowroot Starch (watch the starch however if you have adrenal issues)

Side Notes:

High FODMAPS may disagree with some on the AIP diet. For example; nectarines, coconut or onions may bother some people. Whole30's great Paleo Low FODMAPS shopping list: http://whole9life.com/book/ISWF-Shopping-List-FODMAP.pdf

If you are reacting to certain starches in foods, it may be a sign that high FODMAPS need to be eliminated from your diet. Also, Ashwaganda is in the nightshade family, and should be eliminated during the first phase of AIP. I find it usually well tolerated in general by most people however. If you are FODMAPS sensitive, eliminate for 10-14 days and then slowly reintroduce.

Some Great Reasons To Consider AIP:

  1. AIP (autoimmune disease) is a disease of inflammation that causes self-tissue attack
  2. Food is a powerful way to reduce inflammation and calm the immune system
  3. Diet is usually NOT enough and specific protocols of gut healing and removing SIBO and immune support supplements may be needed
  4. Food is a big component of healing. I believe our beliefs about life is the biggest way to shift the role of disease in our life however.
  5. 95% On The Diet is not on the diet. This is important for when you are starting AIP so you can properly discern what is working and what isn't. I do not believe in failure and our mess-ups are some of the best tools of wisdom we have. If you cannot achieve 100% compliance to the diet, then take it slow, work with an understanding practitioner and know that ultimately there is not such thing as getting knocked off the path in life. You can do this. I know you can. And by 'this' I mean believing in yourself. Forget about right and wrong or success or failure. Do you, your path, your heart. You can't go wrong on that path. (ps. that is part of my program called The Loving Diet™)
  6. Being 100% on the diet makes this program work and makes you a rock star. And if it takes a few try's to get there, you are still a rock star.
  7. IN ADDITION to this protocol, some individuals have food sensitivities, which should incorporated into this diet. If you are sensitive to carrots for example, don’t eat them while on AIP.
  8. Additional Supplements are usually required in my experience to fully heal the gut. Diet is almost NEVER enough to properly heal
  9. I allow green beans, snow peas and sugar snap peas unless low FODMAPS is needed. Because green beans are not mature bean seeds, I allow them. Not everyone in the Paleo world will agree with me about that however and you may consider taking them out during Phase 1. My hard line is no mature beans seeds from the legume family
  10. Brain Chemistry and Adrenal Fatigue are likely culprits in autoimmune disease and need to be addressed. I highly recommend using a skilled practitioner who can properly survey brain and adrenal function and help you. I do not recommend the use of hormones or neurotransmitters in treating brain function (like Melatonin) and advise using caution when using precursors to neurotransmitters. It is my opinion that one cannot treat one without the other.
  11. Undiagnosed Insulin Resistant Hypoglycemia is a big factor in inflammation that can contribute greatly to autoimmune disease, adrenal fatigue and brain dis-regulation. Working with a practitioner who is knowledgeable in ALL of these areas will help you improve more quickly than using 100% diet to heal autoimmune disease.

Eliminating these foods is important to reduce inflammation. All of the above listed foods can be gut irritants and exacerbate dysbiosis in the gut and contribute to SIBO (small intestine bacterial overgrowth). AIP can help address the GALT imbalances (Gut Associated Lymphoid Tissue) in the intestines. Because the gut contains such a large percentage of immune system GALT tissues (70%) that mediate the T & B Lymphocytes that carry out immune system attack by producing antigens or antibodies, the goal of AIP is to reduce this from occurring. It is widely accepted that gut mediated inflammation is applicable for addressing Autoimmune Disease. Below are the studies I have found that link the gut to the immune system. I encourage you to print these articles out and bring them to your doctor.

There are a few ways to approach reintroduction.

  1. 72 Hour Rule: It takes 72 hours to produce an immune response to food antigens depending on which one. It can be physical or mental in nature. Lethargy, brain fog, aching joints, rashes, stomach aches, numbness, feeling hung-over, bloating, gas, constipation, insomnia, fatigue, memory loss.
  2. Re-introduce only 1 food every 5 days and when you re-introduce the food,  eat enough of it to elicit a response. A small bite, then a few hours a spoonful and then that night a serving.
  3. Keep a food re-introduction notebook! I work with many, many people who reintroduce food after a cleanse or AIP and they have a sensitivity symptom and can't remember what or when they did the reintroduction. Writing everything down helps a lot.

I also recommend doing yearly or twice yearly cleanses and support phases, eating fermented foods and bone broth at least 2-3 times a week in 1/2 cup portions. The reason we are compelled to share this all with you, is that food is fun. I believe you can be on the AIP diet and do as a lifestyle. You can be a foodie and do AIP. I love food too much to feel like I cannot eat foods that are satisfying, creative and exciting. Food is spiritual for me. It is my path. Helping others heal is my path. Teaching is my path. As I share my recipes with you, I eat them too. You are not alone in your path to health. We do this journey together.

There are many resources available to you beyond diet and supplements. I talk about them extensively on this blog as well as in my private practice. Looking beyond diet and supplements can be a very valuable endeavor on your path to healing. Here are a few posts to check out:

When You Don't Get Better on The AIP Diet

Self-Compassion and Autoimmune Disease

Trusting Your Life

Autoimmune Disease As Joy In Disguise

New Program for Autoimmune Disease

Illness as Transformation


Other Fabulous Resources (Some are not AIP but useful for autoimmune disease):





By Date


  1. says

    Your AIP diet sounds highly similar to my latex-fruit allergy syndrome diet, but also very different. For your patients who don’t get better on AIP, you might consider latex fruit allergy syndrome. I’ve been in the candida diet and variations of it, low fodmap and the gaps diet, for a year now… and hands down, what helped me the most was finally cutting out certain foods that I absolutely love. Carrots, celery, peaches, pineapple, coconut, strawberries. I already knew that nightshades, soy and wheat were problems, and some fruits and nuts. I already knew that gluten free all purpose flour mndade me feel blah and I never knew why-it’s because of coconut, tapioca, potatoes, garbanzo beans.. After I cut out all those other foods, my chicken skin that I’ve had for forever started clearing up, gives went away, anxiety lessened, and dizziness got so much better. Check it out.
    AIP seems like a great diet though. Take care.

  2. Julie says

    Hi Jessica! I had a question. I recently discovered I am allergic to eggs and since stopping them 10 days ago I feel 10 times better..my anxiety and agitation and horrible depression has gone down tremendously…the depression is mostly gone! I am amazed relieved to have discovered this and will most likely be starting AIP soon. But question for you- I was eating 3 eggs every morning for the past 7+ years. Have you found that some people who are allergic to eggs can have a baked good that contain eggs every now and then and be fine? Thanks for your time! :)

    • says

      Hi Julie! I can’t say for sure. Some can, some can’t. I find it is best to stay off of them for at least 6 months and then try. Glad you figured it out! xx

  3. Debra says

    I am wondering if you could tell me if OCD could be an autoimmune disease. My nine yrs old has been recently diagnosed. I want to look for any ways natural ways to help her before medicating. I have some of the AIP for the past three days (i let her have dill pickles) and her episodes went from at least five meltdowns a day to NONE. Could this really be working that fast? I’m not really sure I am even doing this right. I have done Whole 30 in the past so I just made your adjustments for phase one (except the pickles?) I would appreciate any guidance you could give me as I am desperate to help her feel carefree and happy again.

    • says

      Hi Debra! I have heard of it working that fast, yes. Because doctors tend to not find the CAUSE of the OCD and not diving deep into the physiology behind it, it can be frustrating for parents. You go to the doctor, they listen, then they medicate. They follow the formula they know. There is no searching for what in the child’s physiology could be the culprit. And mostly it is not because there isn’t a willingness on the doctor’s part..but there is just a lack of education of the latest functional medicine available to them. Gluten for instance could be a culprit. Or a severe case of gastritis that affecting the brain-gut axis along with a unknown food sensitivity. There are so many resources and reasons a child could have OCD. Having a brain proficient doctors like Datis Kharrazian Chiropractic Neurologists are very helpful in this regard. Also, Cyrex Labs Panel 10 may be helpful to uncover IgG and IgA food sensitivities. But, yes, it is possible the diet can work that fast and congratulations. There are other nutritional add-ins an alternative doctor can do to continue to the uphill climb! I am assuming they say it is OCD but not tics? So I do not think OCD is an autoimmune disease per say (but Tics can be PANDA or PANDAS which is autoimmune) but everything is related to inflammation and the way the gut and brain communicate with each other. Hope that helps! xx-jessica

  4. Ioanna says

    Hi Jessica! I just wanted to check whether Konjac plant is allowed on the AIP. I don’t know if it may be considered a potato as potatoes aren’t allowed on AIP.

  5. says

    Hi! Great article and lots of great information for clients to follow. I am a fellow nutritionist specializing in pediatric and prenatal nutrition and I love your site!
    I do however have a specification that I wanted to point out with your phrase that it takes 72 hours to make immunoglobulins/ antibodies. I believe you mean that it can take UP to 72 hours to have a non-IgE (IgE being commonly associated with histamine-based reactions or immediate) reaction. Because our mature B lymphocytes (B cells) are constantly creating immunoglobulins that are found in our plasma cells, with IgG being the most common one found in human bodies with a serum concentration of 1240 mg/dl.
    Perhaps you were referring mostly to the immune response? There are two types of humoral immune response: primary and secondary. The primary response begins immediately after the initial contact with an antigen; the resulting antibody appears 48 to 72 hours later. The antibodies produced during this primary response are predominantly IgM.

    A secondary response occurs within 24 to 48 hours. This reaction produces large quantities of immunoglobulins that are predominantly of the IgG class. The secondary response persists much longer than the primary response and is the result of repeated contact with the antigens.

    • says

      Hi Chantal! Thank you for pointing that out. Yes, I meant secondary immune response. I will go back in and correct that. I really appreciate you pointing that out!

  6. Mary says

    I’m starting this diet but my concern is how I will maintain my weight. I am 5’5″‘ tall and weigh 115. The only thing I can see here that would allow me any calories other than just endless servings of meat is sweet potato. I’ve been on this plan for three days and I’m getting diarrhea from so much fiber. Any thoughts? I have some sort of gut problem that occurred after hitting my head a year ago. I’ve had every test and scan known including gluten gut biopsy and no cause found. Thought I would try this. Can’t hurt if I can maintain my weight.

    • says

      Mary, you issue is one for a practitioner to examine…A functional medicine doctor should be able to test your gut properly and get to the bottom of why what is happening is happening. take care, jessica

  7. Libby kavanagh says

    Hi Jessica, my 20yr old daughter has recently developed alopecia areata and I’m trying to figure out the most effective way to treat her condition. Do you feel that this lifestyle diet would benefit her and have you had any success with others with this condition?

    • says

      Hi Libby!
      Diet is just one piece. So yes, I suggest it, but I also suggest finding a person that can help with everything. I have seen great results from AIP and alopecia, usually in combination with other factors like healing the gut, etc. Hope that helps!

  8. Donald says

    I completed the Whole 30 program in June/July then I fell off of the wagon for a while and now both my wife and I are on the AIP program with 120% commitment. I very much struggle with unconventional breakfast, I’m a toast and granola kind of guy but we are into the second week of the program and we are settling in nicely except I’m suffering from what I would refer to as gut rot. Just an uncomfortable feeling I get when my protein intake goes up. What is it and what foods would counteract this feelin. It’s definitely worse in the morning.

    • says

      Hi Donald! Perhaps you need digestive support for protein? I would ask your alternative health care doctor or nutritionist to help you with that…
      so happy to hear you are trying AIP! Would love to hear how it goes after you and your wife have been on it for a few weeks! -jessica

  9. Bella says

    Hi, I’m wondering if the AIP would be helpful for me. I’ve been positive for ANA for years, with my most recent titre being 1:640. However, my doctor can’t seem to find me positive for SLE or any specific autoimmune disease, even though I’m exhausted all the time and get an achy back and low-grade fevers. He seems to think I definitely have autoimmune issues though. I guess since its inconclusive, I’m hesitant to try AIP. I also have been suffering from greater depression, anxiety and huge weight gain recently. Thank you for your opinion.

    • says

      HI Bella! I am so sorry this has been hard. I am wondering if you found a more holistic doctor that can expand the testing you have had to be more comprehensive? You can search Functional Medicine Institute website for doctors by state. I would try that!

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