Stacy's Autoimmune Protocol Results

Before I begin this post, offering my results, links and information on the Autoimmune Protocol of Paleo work, let’s take a moment to thank Diane Sanfilippo for creating her definitive guide and information source on all variations of applying a customized approach to Practical Paleo living. For, if it hadn’t been for her book, I likely wouldn’t have figured this all out.

Today, her book was announced as a New York Times Bestseller, a title held by only 2 other paleo books. I cannot congratulate her enough. I am thrilled to personally know Diane and am in awe of her never-ending desire to help heal people through nutrition and lifestyle. Her book is a literal masterpiece and the fact that it’s available to the random person searching for answers at Target, Wal-Mart or Costco blows my mind.

I remember the scene when Cordain’s book was the only one out there, and seeing the progress we’ve made in 2 and a half years give me hope. It gives me literal motivation and a desire to keep trucking along and using our voices the best way we know how, too.

The point to all of that, in case you’re skimming, is that although I’m going to tell you my opinions and n=1 experiment results in this post, it’s Practical Paleo that helped me figure this all out. So, if you’re remotely curious – go check it out from the library or buy it for yourself. I don’t think there’s a single person in this whole world that wouldn’t benefit from at least parts of that book.

Preliminary Reading

I get asked, almost on a daily basis, “what is Autoimmune protocol?”, “Why can’t you eat eggs on Paleo?” and a host of other questions I’ve already answered on this blog. So, I’m putting all the info below in order for you not to have to search around for it. You can also search by the Autoimmune Tag we created for more.

If you recall, I decided to go on the autoimmune protocol in my Stacy WTF post
Then I talked about reading Practical Paleo and going Egg-Free as a result
I went on even more about how Practical Paleo AI’s section helped me in my review of the book
Lastly, I blogged about how AI Paleo helped me with Beating Post-Nursing Depression

The Paleo Mom and I did an entire Autoimmune podcast, which we each told our stories and recommendations (even if you don’t listen, the show notes have links & info)

After realizing how limiting food choices were, we posted a bunch of recipes that worked within the parameters of my limitations:

Chewy Molasses & Ginger Cookies
Creamy Coconut Chocolate Chip Macaroons
Banana Pumpkin Pucks
Creamy Dreamy Frozen Custard

Against All Grain’s Breakfast Cookies
Urban Poser’s Berries & Cream Breakfast Cake

Stacy’s N=1 Foods

As you can see by some of the recipes linked above, they include chocolate chips, sunflower seed butter and egg yolks – all usually eliminated in the Autoimmune paleo protocol. The good news for me is, after being paleo for 2 1/2 years and having done a STRICT 30 day autoimmune protocol – I was able to reintroduce those foods with little to no impact!

The bad news? I’ve realized that I cannot yet reintroduce nightshades, nuts or egg whites to my diet. The grey area? Spices, butter/ghee and coffee. I realize I have a slight reaction – but sometimes the benefit outweighs the cost.


Reintroduction is done by adding in ONE eliminated food in 2 or 3 meals in a row in a large enough quantity to produce a result. Wait a few days and see if you have a reaction.

My major signs of my autoimmune issues are tingling skin around the mouth, facial acne, joint pain, headaches and the “every body out” gut reaction. Everybody’s results are different – so listen to your own body. The Paleo Mom recently posted about reintroduction of foods on AI if you want more info.

I happen to know two incredibly smart and talented people who are working on more complete reference and resources for autoimmune, so you’ll have something better than just blog posts soon! In the meantime, I posted (a long time ago) about the list of what conditions are Autoimmune – even Type 1 diabetes could potentially benefit from evoking this protocol!

My Results

I feel great. I crack my knuckles and joints less. I rarely get a headache and (most importantly) have perfect eliminations! Oh hush-up if you’re squeamish; this is an extremely big deal for someone with Celiac and without a gallbladder!

I believe I finally have significant progress on healing a leaky gut. I believe my body likely responds to nuts, much the same way it does legumes and grains – immediate gut reaction. I didn’t have gas after I ate nuts before, but I do get it now. So clearly, digestion isn’t going perfectly.

As a Celiac, I will likely always have a leaky gut – so whatever I do to help it heal as much as it can is a huge step in the right direction. With going nut-free for so long, it has been a huge help!

Nightshades and dairy are a joint and skin issue for me, rather than digestive, so I’m a little more forgiving of myself if I end up with spices or butter in my food. Long term, it’s not causing huge damage to occasionally have minor amounts of both. However, I unfortunately will probably never sit down to a huge bowl of tomato soup without feeling and looking awful the next day.

Recent photos of my skin & nails – sans issues!
p.s. I did not eat that rice, only a huge amount of ribs – also, that lovely red hair color is courtesy henna hair dye!

The true test for me was when I got glutened last week (we’re renovating our house and have been eating out a lot, cross-contamination happens when we sometimes try new places) and my reaction was minimal. I was nauseous and had a headache – but after a good night’s sleep it was gone. I had emotional problems, as I’ve described before as the gut-brain reaction I have, but it only lasted 18 hours – instead of the 3-7 days I’ve experienced before. And my severe gastro-intestinal problems didn’t even happen!

I honestly couldn’t believe how amazingly my body responded. Beyond the relief of facial acne and joint pain as well as improved hair, nails and skin – it was clear to me I need to treat non-autoimmune foods the way I treat non-paleo foods, because my body thinks of them all as equally bad.

It’s a Lifestyle

Just like paleo, the autoimmune protocol is now a forever lifestyle for me. I take pride in the fact that most people in my life have no idea of my further limitations. It’s a lot for even Matt and I to keep track of, I don’t want to overwhelm anyone.

It’s an important distinction between paleo and autoimmune paleo. It can be overwhelming for someone else to thinkย  about (no grains, legumes, dairy, refined-sugar, eggs, seeds, coffee, chocolate, insoluble fiber, nuts or nightshades – including spices). If they didn’t know what to cook for you or what restaurant to choose before, imagine their horror if you tell them all that!

I’ve finally figured out how to integrate it into my lifestyle (spices and butter were huge for this) so that I’m not trapped by only eating at home. But it means I make conscious decisions to make lifestyle decisions daily to help my body heal.

Do I enjoy slathering myself in fermented cod liver oil and ingesting it daily? Not my favorite thing. Is it embarrassing to pull out a huge container of supplements at every meal? Of course. Do I feel sexy going to bed with fermented fish oil on my face? Not exactly. But that’s not what matters! I’m healing myself and I’ve prioritized ensuring I take care of me.

I MUST sleep. I MUST exercise.

First of all, how exciting that for the first time since bringing out this strong autoimmune response with the stress of finishing Eat Like a Dinosaur and Wesley weaning, that I finally have energy and a desire to exercise!

Going on walks with the boys and doing yoga with a DVD in the basement with the boys joining me has been one of the most personally rewarding and enjoyable things in my life. By figuring out how to implement psychical activity in my life, I saved myself an hour from going to and from the gym, and I added quality time with my family by having the boys join me in the mornings!

In order to make time for these things, I often find myself saying not to friends who are having parties, inviting me to yoga classes or wanting to hang out and do stuff. Saying no to fun sounding things can be frustrating; but, I know it’s for the best in my long-run. I find that if I plan activities, I can work around my own limitations and then ensure I’m not over doing it.

I’ve learned that the simpler my life gets, the better I feel. I reduce chemicals, I decrease stress and energy and joy become elevated. Seriously, listen to this part. I believe it’s a huge factor we can all control – affordably, albeit not at all easily. I took stress management extremely seriously and it has been a huge contributor to my improved health.

Should You Do It Too?

If you’re just starting your paleo journey, the idea of giving up sweet bell peppers, eggs, nuts and paprika could make you want to abandon paleo completely. I remember reading “eggplant isn’t paleo” on a forum when I had just started and got SO confused and frustrated by what I was supposed to be doing and what it all meant.

Please don’t think this is required for paleo! This protocol isn’t for everyone, and in my (non-professional) opinion, I strongly believe it should only be implemented after standard paleo has been going full-swing for 3-6 months.

Paleo from SAD or even basic gluten-free diet is going to be a huge improvement and relief for your digestion and immune system. With paleo, inflammation will go down, gut will begin to heal and (my guess is) you will feel much better – even if you have an autoimmune disease.

Just know, if you have an autoimmune condition – or anything that’s still weird and lingering after going paleo for quite some time – that doing the AI protocol for 30 days could help you!


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  • Meredith

    congratulations on your progress! it’s inspirational!

  • Sara Grambusch

    I’m glad you had such a great experience going AI. Diane’s meal plans are so great. I don’t have all my digestive issues totally fine tuned yet but I’ve kind of forgotten that fruit and nuts are “paleo” at all because I’m pretty sure they’re not my friends. It is really hard to constantly eliminate things but we just have to keep the big picture in mind, which is certainly why we found paleo in the first place, for our health!

  • Julie

    Thanks for the update on your progress. I know I have AI issues, but I’m still trying to get Paleo down before I cut out even more. I was recently tested for basic allergies, and found that I have sensitivities to all grains (was not surprising at all, especially the corn and soy), however it showed no reaction to gluten, so that was interesting. All I know is that grains are bad for me personally and my body doesn’t like them. So I keep going forward. As always, your journey is inspiring! Thank you so much for sharing.

  • Stacy M

    Amazing and inspirational. Thank you so much for sharing.

  • Lindy

    I’ve been strict paleo for almost two years and suffer from the autoimmune disorder Ankylosing Spondylitis (spinal arthritis with gastro complications). I think all these paleo baked goods are too hard on our systems. Looking at those recipes, I can’t eat dates, molasses, bananas, sunflower seeds, arrowroot (yikes…absolutely nothing starchy), applesauce (apples…FODMAPS), cherries, cinnamon, chocolate, and coconut flour is the hardest thing to digest in my opinion…it’s like lead in the belly (and I was just in the emergency room for acute gastritis/gastroparesis after drinking some coconut milk to try to increase my weight). While I know people work hard to figure out substitutes, I think those of us with chronic illness need to drop all this and stick to the basics: meat, broth, and no-starch veggies for the healing process. I’m weary of paleo cookbooks trying to help us by offering things that don’t work either. It’s better to admit a tough-love couple of years and stick to it.

    • I’m with you Lindy! I can only tolerate a small list of veggies in addition to broth and meat because I have SIBO. I’ve been working on writing an autoimmune protocol cookbook with modifications for those of us who can’t do all of the FODMAPs and starches, because I find there are plenty of us out there and not a lot of support for it. ๐Ÿ™‚

  • Thank you for this post. As is true of so many of your posts, this one helps to make these big changes manageable. My family found Paleo due to intolerance testing. Many of mine fall in line with some of the AI protocols and knowing that there are other people out there like me and that life goes on is quite helpful. Thank you for this!

  • Sheryll Ziemer

    Horray! You have got to be so proud of yourself for what you’ve gone through, to get to where you are currentlyt. I love to read your blogs, because I’m on a journey for better health too. There is generally not enough information out there for people who have autoimmune disorders, and certainly a general practitioneer can’t help because they have NO education on dietary needs. We have to rely on ourselves and by sharing what you have, you’ve made it so much easier for the rest of us. Now we have some guidelines and we know there is help. Thank you Stacy!!!

  • Sarah

    That picture showing off your henna hair dye? You look AMAZING! Truly beautiful and so young. Obviously, your health is shining through!

  • Kate {Eat, Recycle, Repeat]

    “The simpler my life gets, the better I feel.” I couldn’t agree more. What a great philosophy!

  • Lynn

    What do you mean when you say that celiacs’ will always have leaky guts? I have celiac; am I doomed to a leaky gut forever?

    • By virtue of the fact that you have an autoimmune disease, you may always have the symptoms of a leaky gut. That’s why it’s so important to do everything in your power to avoid eating reactive foods. Good luck!

      • Lynn

        I thought that celiacs could heal their leaky guy by carefully following a GF diet and avoiding foods they are sensitive to?

        • From the research I’ve read and heard, Celiacs have a widening of the joints in the gut – which is what causes leaky gut – anytime they are exposed to gluten or for most a cross-reactive food. So, although Stacy being on AI for so long has helped her leaky gut, every time she has an exposure or cross-reaction or eats a non-AI food, it causes the gut to weaken and joints to widen because her system is wired that way. For some, they “heal” a leaky gut and can have exposure and the joints don’t automatically widen – this is the philosophy of GAPS. But, for those of us with AI conditions – our body is built to never want that stuff and will have a similar reaction each time you do.

          I’m not a scientist or doctor, simply restating what I’ve heard and experienced myself. So if you have research that you believe is counter, then go with that… it’s all a learning journey for us all ๐Ÿ™‚

          • Lynn

            That makes sense. I always say it is impossible to be 100% GF unless you grow all your own food and butcher your animals. I mean, people picking the fruit and veg may have just had a sandwich for example. So I guess I’ll need to expect improvement rather than perfection from my GF whole foods diet.

  • This is an awesome post. I also have celiac as well as hashimoto’s, and have been on the protocol for a few months now with modifications for SIBO. The only things I have reintroduced successfully are egg yolks and some seed spices. I have the same reaction you describe with nuts. I feel great and don’t intend on going back to plain paleo! ๐Ÿ™‚

  • Stacy: Thank you for this blog- I’ve been following it, and you inspired me to buy Practical Paleo. You state that you think people should be paleo for 3-6 months before going on the autoimmune protocol. What’s the reasoning behind that? I’ve been gluten/refined sugar free for about 2 years now, and suffer from Hashimoto’s Thyroiditis. My iron is not converting correctly because of some undefined systematic inflammation, so I have low iron and high ferritin. Anti-inflammatory measures (stress reduction, exercise, supplements) have not worked to this point, and I’m now thinking the key might be leaky gut.

    • Only because it would be hard to jump right in without prior training in avoiding the regular paleo foods. If you think you can handle jumping right in, by all means!

      • Thanks, Stacy. I think doing the AI protocol might be what my body needs, and I can find out if and what needs to go for good. BTW, you look like you feel great!

  • Great article. Thank you for the last paragraph. I have MS and trying to go Paleo AI sounds like i might fail. So I did start Paleo a week ago and I’m good right now…..family is 50% on bored but im the one cooking :).

  • I recently discovered I have a sensitivity to nightshades. Curiousity question: have you ever known anyone with autoimmunity who is sensitive to just one nightshade instead of the whole group?

    • I don’t think we’ve heard of anyone with sensitivity to just one nightshade, but there is usually a spectrum of differences in the reaction to different kinds of nightshades. For example, tomatoes are the most reactive of the nightshades for many many people, but often you’ll find little reaction to potatoes. Hope that helps!

  • One more question: Like Stacy, I’m learning that my body doesn’t do too well with nuts, so I’m going to reintroduce seeds instead this weekend. Do you find there’s a difference in how your body reacts to seed butter vs. soaked seeds vs. toasted seeds? I’m just trying to decide whether to reintroduce them all as one big group, or go in stages based on how they’re prepared.

    • I’d look into Practical Paleo’s recommendation for reintroduction, all at once is NOT recommended because then if you flare you don’t know what caused it. Definitely soaked, sprouted and/or dehydrated nuts/seeds affect me less than raw.

      • Thanks for sharing your experience. That information isn’t in Practical Paleo. In fact, no one seems to go into detail on the nuts/seed reintroduction (at least not that I can find), so I’ve been taking a poll to try to gather experienced advice. I appreciate your input!