The Epidemic of Autoimmunity
Autoimmunity is a 21st century epidemic, especially in the Western developed nations. Most likely, you have a close friend or family member with an autoimmune disease – or maybe you have one yourself. The American Autoimmune Related Diseases estimates that 50 million Americans suffer from an autoimmune disease.
Why is autoimmunity so prevalent? As Hippocrates accurately said, All disease begins in the gut. Our modern diet and lifestyles cause permeable digestive tracts so that we are prone to develop autoimmunity or have a child with a predisposition for autoimmunity. Understanding the root cause of autoimmunity is key to healing it, so we’ll go into more details in a moment.
The good news? When it comes to addressing autoimmune diseases, diet works. And I’m living proof.
Healing my own autoimmune disease
As you may know, I struggled with a severe form of ulcerative colitis, an autoimmune disease. I quickly gained remission and was able to stop my medications after starting the GAPS Diet, a popular protocol for autoimmune disorders.
While the GAPS Diet absolutely turned my life around, it took a year of experimenting before I found foods that were impeding my healing process. I found my problematic foods included egg whites, nuts, seeds, and nightshades. Recently, I learned that I had modified my diet to closely resemble the Autoimmune Paleo Protocol (AIP), a dietary regimen for treating all variations of autoimmunity.
The Autoimmune Paleo Protocol
I began learning about the AIP first through Sarah Ballentyne’s site, The Paleo Mom. Sarah is a scientist delves into details about exactly why the AIP works. Quickly afterward, I found Mickey Trescott (that’s her on the left!), author of The Autoimmune Paleo Cookbook and the blog Autoimmune-Paleo.com.
I asked Mickey some questions about the AIP to give you an overview of the protocol. You can find even more information about the protocol on her site and The Autoimmune Paleo Cookbook, which I review below.
What foods are included in Autoimmune Paleo Protocol?
Mickey:
Strictly avoid:
- Grains (including pseudo-grains like quinoa)
- Beans and legumes
- Dairy
- Eggs (of any kind)
- Nuts (including chocolate, unfortunately)
- Seeds (including coffee and seed-based spices like coriander and cumin, and seed oils)
- Nightshade vegetables (tomatoes, bell peppers, hot peppers, eggplant, potatoes, and spices derived from them like paprika, cayenne, and curry)
- Food chemicals and non-nutritive sweeteners, including stevia
- Alcohol
- NSAIDs
Include:
- Pastured meats like beef, chicken, turkey, lamb, duck, and bison
- Bone broth and organ meats from pastured animals
- Wild-caught fish and shellfish
- Animal fats like tallow, lard, and duck fat from pastured animals
- Tropical oils like coconut and red palm (sustainably harvested)
- Olive oil and avocado oil (for cold applications)
- Any fruit (except ground cherries and tomatoes, which are nightshades)
- Any vegetable (except nightshades, denoted above), especially leafy green veggies, roots and tubers
- Herbs and spices that are not seeds or nightshades, like thyme, rosemary, turmeric, garlic, ginger, etc.
- Coconut flakes and coconut butter
- Vinegars, like apple cider, ume plum, or coconut
- Fermented foods like saurkraut, kombucha and water kefir
Here are handy reference lists with print-out guides to stick on your fridge.
How does the Autoimmune Paleo Protocol support healing?

From the book
Mickey: It has been shown recently in studies that all autoimmune diseases have one thing in common – intestinal permeability, otherwise known as leaky gut. When the gut lining becomes permeable, undigested particles of food, toxins, and pathogens are let into the bloodstream, thereby triggering the immune system. All of the foods avoided on the autoimmune protocol are those that have been shown to exacerbate leaky gut, and strict avoidance gives it a chance to heal.
In addition to this, the autoimmune protocol is an extremely nourishing, nutrient-dense diet and contains all of the nutrients needed to heal the gut lining, as well as the other parts of the body that have been broken down and inflamed by autoimmune disease. Once a person experiences a measurable improvement, they can then reintroduce foods to see which ones are contributing to their symptoms, ending with a unique diet that promotes the maximum amount of healing for their bodies.
Who is a good candidate for the Protocol?
Mickey: Anyone who has an autoimmune disease should try the autoimmune protocol, regardless of what organ or tissue the autoimmune disease affects – thyroid, skin, joints, connective tissue, and so on. In addition, anyone who suspects that they may have an autoimmune disease or has undiagnosed symptoms should try the autoimmune protocol.
The protocol is not a quick-fix – learning how to promote healing by trial and error is a long process and not for the faint of heart, although it is incredibly rewarding.
How much room for flexibility in the Foods to Avoid is there in the AIP?
Mickey: Unfortunately, there is no flexibility in the elimination diet. While some people choose to ease their way into the protocol, once all of the foods are eliminated a person must be 100% strict in order to have the best chance of making progress. This means checking the ingredients of everything – including teas, supplements, and condiments, as well as being extremely careful while eating out or at someone else’s house.
Once the elimination diet is over, a person can then reintroduce foods systematically to find out what their tolerance is to the various un-allowed foods, but until they get to that point, they need to be 100% strict.
How long should one follow the Autoimmune Paleo Protocol?
Mickey: I generally recommend people start with a month for the diet, but it is best not to reintroduce foods until you feel a measurable improvement in your symptoms. This could take anywhere from a month to over a year (rare, but I have heard of it happening!) Otherwise, it is very hard to tell which foods are affecting you when you go to reintroduce them.
Some people start to feel better, and they continue on the elimination diet because they want to keep healing. This is the approach I took – I reintroduced a few foods (nuts and seeds) a couple of months in, but waited a fairly long time (1 year) to reintroduce eggs. I still haven’t been able to reintroduce grains, dairy, or nightshades, and it has been 2 years.
What should one eat if one decides to transition off Autoimmune Paleo Protocol?
Mickey: I recommend people transition to a standard Paleo diet after being on the autoimmune protocol, and I think it is important to continue to include fermented foods as well as organ meats and fish. It is very important for those with autoimmune disease to stay grain-free, at the absolute minimum.
I think adding certain foods to my diet, like homemade bone broth and organ meats, has been as helpful as removing certain foods. How to these foods fit into the AIP?
Mickey: The Autoimmune Protocol is as much about the additional healing foods as the foods that are avoided. Bone broth, organ meats, fatty fish, and ferments are all an important part of the protocol, and those that do not include them do not progress the way that those who do. All of these foods are incredibly nutrient-dense and contain the raw materials to heal the gut and promote healthy flora balance, which is what the Autoimmune Protocol aims to do.
What is the AIP approach to sugar consumption?

From the book
Mickey: The Autoimmune Protocol is not a sugar-free diet, although refined sugar and excessive fruit consumption is not allowed. A piece or two of fruit a day is perfectly fine, provided it is well tolerated. I don’t advocate making treats or using sweeteners like maple syrup or honey on a regular basis, but they are fine for occasional use (maybe once a month).
I use fruit in some of my recipes for flavor and to add a touch of sweetness, but they always appear in the context of adequate fat and protein (like some citrus in a pot-roast, or cranberry short-ribs). Blood sugar issues are well known to cause autoimmune flares, so I stress that people take it easy on the fruit and treats without completely depriving themselves. It is about balance!
Finally, how has the Autoimmune Paleo Protocol affected your own health?
Mickey: I came to the Autoimmune Protocol after I had been diagnosed with both Hashimoto’s and Celiac disease. I had been vegan for 10 years, and I had a massive crash that left me bedridden and unable to work for months. Out of desperation I decided to try the Autoimmune Protocol, and finding out about my food sensitivities turned out to be the thing that enabled me to find health again. It was a long road, and I am still working on healing my gut two years later – but it has absolutely changed my life!
The Autoimmune Paleo Cookbook
Are you ready to heal your autoimmune disease through diet, but overwhelmed with the idea of this protocol? I totally get it. It takes a lot of courage to make these drastic changes – both Mickey and I understand this! If you are ready to make the commitment to heal, then I strongly encourage you to look at Mickey’s book, The Autoimmune Paleo Cookbook, an essential guide for the protocol.
Here’s some of the highlights in this guide:
- A detailed explanation of the Autoimmune protocol
- Multiple AIP friendly meal plans with shopping lists
- Step-by-step guides for preparing staples like bone broth, probiotic drinks and coconut products
- Over 110 creative, straightforward, and delicious recipes for the protocol
- Gorgeous photography by food photographer Kyle Johnson
- Extremely tasteful layout and design (a point oddly dear to my heart… am I the only one who judges a book based on the graphic design?)
Don’t forget to check out the other wonderful resources and free recipes on Mickey’s site!
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When you discuss no diary, does that mean almond, cashew or coconut milk?
Is egg whites allowed more so than eggs with yolk?
I have Sjogrens syndrome and I’m looking for ways to heal the inflammation, gut issues, energy issues that I have and need to change.
This information was very informative and I thank you. Any suggestions you can give would be great.
Hi, just curious about this as we have an UC and PSC sufferer in the family and on research years ago I found the Breaking the vicious cycle book or should I say the eat well feel well book and there is some contradicting food advice there to what is suggested here. Not that he would change his diet anyways he point blank refuses as he does not believe in it, and neither his gastro nor his hepatologist recommend or suggest any kind of diet modification seeing he does not smoke or drink, they think smooth sailing take your medication…. but I find myself looking for answers, alternatives, new thing, continuously. And no matter what I find, everyone swears by it, but contradicts other similar approaches. I think maybe it is too individual to suggest a one diet fits all approach? After a brother on his side was also diagnosed I grow more concerned about food and diet especially for my kids and I am very aware of “good and bad” foods, over processed, GMO’S etc….but I am so confused and kind of at a loss here, no idea what to do or where to start….(We are in Ireland)
Oh he is also told not to take any supplements to boost immunity (understandable I suppose) and no vitamin/mineral supplements either ….
How do you know if you have an auto-immune disease??
My condition: dysbiosis, candida, heavy metals, hand eczema, adrenal fatigue, low progesterone and low DHEA, estrogen dominant
I’m concerned about these diets and body pH levels: diets that emphasize animal proteins can cause the body to become acidic, fostering disease and candida.
I have been following the anti-candida diet for the past six months. A few weeks ago, I tried eating a fourth cup of green apple and experienced bloating and brain fog for days after. Same with sprouted wild basmati rice. So it seems that my body is not tolerating sugars well, but I don’t know how long I’m to follow this diet (or GAPS, or AIP, or SCD), especially considering the liabilities.
Thank you so much for this information. My body tends to have a very high inflammatory response. I have a number of chronic health conditions ever since I was a kid, ranging from asthma and lots of allergies to various GI issues, neuro muscular, thyroid, severe skin problems, and cognitive, memory and sensory processing issues. Several years ago I started seeing an immunologist who has developed a new marker which identifies individuals who have this high level of systemic inflammatory response. My mom, who had Alzheimers, my daughter, who has Autism and Epilepsy, and myself all tested with very high positives. We also learned about certain food sensitivities. Based on that we all cut out dairy, soy and gluten and a modified candida diet. We saw a lot of improvement. However, lately it is clearly not enough for me. I have been having very severe outbreaks of a blistering kind of ecxema , I can hardly walk and it’s very painful. My immunologist is recommending IVIG. After reading about the AIP diet, I just have this gut feeling (sorry, no pun intended) that this could really help. Here is my dilemma. My daughter is already doing the ketogenic diet recommended by her neurologist to control seizures. It really seems to be helping with that. I just feel daunted by doing two different difficult diets that oppose eachother at various points. My daughter’s fruit and veggies are much more limited than on AIP and she gets upset if there’s stuff in the house she can’t have. Remember she has Autism and is only 11. Meal planning is also very challenging as she can overload on Eggs with her diet and can have nuts and I can’t. There are some similarities, but enough differences between the diets to be very overwhelming. Any thoughts or suggestions? And I apologize for the length. I thought having a better understanding of our situation would help.
What’s wrong with eggs?
My painful, prevalent psoriasis healed once I found which foods triggered it through strict adherence to AIP Paleo and slow, methodical reintroduction of foods. Amazing!
This diet is only geared to paleo and animal product consumption I feel there needs to be a vegan version as all the studies I have read are that all animal products including dairy are highly acidic in the body and acidity creates disease