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!
Does anyone know if this works for Cns vasculitis pacns ,
Do you know anyone got better using this approach
Did you try it Mark K?
I’ve been on GAPS Diet for over 2 years now for ulcerative colitis. I did a long slow Intro Diet that lasted 5+ months. I initially seemed to be doing fine with the fermented dairy, nuts, seeds. In addition, I’ve had major PMS issues my entire life, including bouts of heartburn and vomiting the last 2 weeks of my cycle. On GAPS, that went away, until I had to eliminate dairy for a completely different reason. It was several months until I realized that my PMS symptoms returned when I eliminated the fermented dairy. I started slow, with adding in ghee and then a month later butter, and then from there started adding in the various fermented dairy products. As soon as I added the dairy, the PMS related vomiting stopped. However, a few months later, I realized I was having major colitis issues and a flare up of an excruciatingly painful anal fissure. What had changed in my diet? The dairy. UGH! So I took back out all dairy other than the ghee, which I now only eat a few times a week (trying to find balance with it so that the PMS vomiting doesn’t start back up). It has been 4 months now and I’m still dealing with the flare up of the fissure, along with colitis flare ups. I realized that it seems like I have now developed an issue with seeds and nuts, and even coconut flour is problematic. When I was in my first year of GAPS, I had no issues with any of those foods. So now I’m wondering if GAPS is causing even more problems, since I didn’t have those food issues back closer to the beginning of GAPS. I even seem to be having issues with all kinds of vegetables. And I’m now looking to move away from GAPS, whether that means eating the foods allowed on PALEO or trying the WAHLS Protocol,I don’t know.
What I have found about lupus and diet is that diet without preservatives almost totally reduces the quantity of symptoms. You could find out more here:
http://bit.ly/10JoAcO
Hope that helps someone.
I love Mickey’s cookbook and found the information she provides very helpful, and I’m glad to see her cookbook promoted on other sites.
I do have to say, though, that if you’re going to use photos from her cookbook in your posts that you should at the least give credit to Mickey / the cookbook photographer Kyle Johnson and should definitely not place your own logo on one of Kyle Johnson’s images and then publish it to Pinterest (how I found this page) without proper credit to him. Simply mentioning his name in relation to the cookbook at the end of your article is not appropriate attribution. How can I trust that the content on your site is reputable when you are not even properly crediting your sources?
I’m interested in this diet approach, although realistically, I think I’d find it very hard to stick to but I the doctor thinks I have Hashimoto’s, to join the Type 1 Diabetes, Vitiligo and Alopecia Areata that I already have fun with.
Can this type of paleo diet help all these autoimmune conditions? How do I deal with a diabetic hypo if I can’t use sugar that quickly corrects a hypo?
Thanks in advance for any advice on that one.
Hi! I was diagnosed with Graves Disease last April. I was so sick. I went to see an acupunturist who suggested that I eliminate dairy. I felt a bit better, but was still having joint pain, hair loss, extreme fatigue, and eye issues. I had a celiacs test that came back negative, but once I eliminated gluten, things really began to change. I also noticed that many beans and lentils irritate me, so I stopped eating them. I am happy to report after three months on a modified version of this diet, my blood work is normal! It’s been a difficult transition as I was a vegetarian for 14 years. I can eat fish with no problem, but chicken is so strange for me. I also had a piece of bacon the other day and I liked it. My health is improving every day and I plan to stick with it.
Hi,
I’m on AIP.
How do you know, that you still have to work on healing your gut?!
Thank you!
Hey, I’m gradually preparing myself for this diet and will get the book as soon as I can but I have a question. I have gone gluten free already and decided to have some lentils for dinner yesterday. That same night and into today I’ve been having excriciating joint pain. I was only expecting gluten to have this effect but the lentils seem to be causing me joint pain. Anyone experience this?
If I have had IGg testing done, and have no response to some of the AIP food, not to eat, is it ok to eat them? Eggs is definitely a no go for me, but some of the others hade no response at all (IGg)
Hi,
I was due a colonoscopy today and somehow there was a mix up with my appt at the hospital… so I came home feeling down… I was told to increase my meds for my UC again. I decided to research a little online and your website and your words have given me HOPE. I am going on holiday soon but once I am back ( in like 3 weeks time) I plan on starting to follow this diet. The no Alcohol part may be difficult at the weekends but I want to overcome this condition badly! I am on 6 tablets a day including suppositories a few times a week. Its tiring…..
So the first thing I guess to do is purchase The Autoimmune Paleo Cookbook right?
Thank you for your words once again. I am 25 and do not want to live on tablets my whole life.