The Autoimmune Paleo Protocol Is Scary

IntimidatedThe “Autoimmune Paleo Protocol” can be pretty intimidating. I know this because I get emails from nervous people saying something along these lines…

“Do I really not get to eat eggs anymore if I have Hashimoto’s and I want to eat Paleo? Really? I’d rather cauterize my eyeball with a burning hot fried egg than not eat eggs anymore. I mean, no eggs? Come on! No tomatoes, bell peppers, nuts, or seeds, either? And all this on top of the no grains, legumes, dairy, or sugar that the normal Paleo diet recommends? That’s ludicrous!”

And it is, especially to people who are just starting out this whole change-your-diet-to-heal-your-body thing. It sounds awful and scary. Maybe you’d rather have joint pain or fatigue or unexplained weight gain for the rest of your life than change such an integral part of your life so drastically.

But I have good news for you!

You don’t necessarily have to do the autoimmune protocol!

Let me explain.

Here’s what Robb Wolf has to say about the Autoimmune Paleo Protocol:

“Some of these otherwise Paleo-friendly foods have been shown to be problematic in individuals with autoimmune issues. We recommend you fully remove not only these foods but also all Neolithic foods (grains, breads, potatoes, beans and dairy) for at least a month to see if they pose a problem for you.”

And it’s true. There are studies that show that the lysozyme in eggs, the saponins in nightshades, and the phytic acid in nuts & seeds can wreak havoc on our guts and increase gut permeability (leaky gut). Gut permeability is the reason we get autoimmune diseases in the first place. When your gut gets “leaky” and it starts letting food particles into your blood stream that shouldn’t be in there, your immune system starts to react.

Sometimes those food particles look like parts of your own body (like your thyroid, your intestinal cells, etc.) and your immune system starts attacking those cells – your own body’s cells – as well as the food particles. That’s autoimmunity in a nutshell (no pun intended).

But – and this is a big but – we are all special snowflakes and we all have our own tolerances and sensitivities to different foods. And telling someone to go from zero to remove-all-your-favorite-foods-right-now is not necessarily sustainable advice. They’ll say, “No f-ing way, buddy. Not gonna do it.” And then nothing will change because they think if they don’t do the Autoimmune Paleo Protocol right now with zero compromises, nothing will improve.

There is another way that may very well improve your situation: moderation.

I mean, by all means go for it and do the autoimmune protocol if you want. But if you’re totally put off by that idea, take this thing one step at a time.

  • My advice is to start with a regular Paleo diet. Take out the grains, dairy, sugar, legumes, and vegetable oils.
  • If that’s too hard to imagine, hell, start with just removing grains from your diet and see if you start to improve. I bet you will. 
  • If even that is too much for you, start by just going gluten free, and I have a feeling that you – like so many people before you – will start to feel better. Eat rice, tapioca, quinoa, buckwheat, and all the other gluten-free grains, instead of wheat for a while. Gluten is probably the biggest culprit of them all in our inflamed gut issues, so if you’re looking for the smallest, most unnoticeable change to your diet to help your body heal, go gluten free.  

This is not my normal gung ho way of being or writing – I know. I think Van life is making me soft. But if I’ve learned anything over the years working with clients and talking to you all, it’s that some people just aren’t ready. Some folks just don’t want to disturb their way of living that much, even if it could mean miraculous healing. It’s just not worth it to them.

And that’s ok!

Start small.

If you find you’re seeing results with your first dietary change, but you still have symptoms, keep moving toward Paleo. If in 6 months you’re full blown Paleo but you still have a few symptoms here and there, stop eating eggs for a couple weeks and see how you feel. If that doesn’t make a difference, then start eating eggs again and try taking out nuts and seeds. Do the same with nightshades if you want to experiment further.

If you’re not the kind of person who can take it all on overnight, don’t beat yourself up about that, and know that even very small changes to your diet can make a huge difference.

Figure out where your threshold exists between eating the foods you love and feeling vibrant and healthy.

What do you guys think?


I almost forgot. If you ARE ready to take on the Autoimmune Paleo Protocol, we have a meal plan for that in our 21 Day Paleo Cleanse eBook. I go into more depth about this whole topic, and we make it easy for you to cook and eat without eggs, nightshades, and eggs with 3 weeks of meal plans and grocery lists. Here’s the link



  1. You couldn’t promote the Autoimmune Paleo Plan in the Winter? I wait all year for home grown tomatoes and peppers. I LOVE Gazpacho. Now the only part of it I can have is cucumbers and onions??? It’s just cruel. I would love to feel better though, and walk without a prop (I refuse to call it a cane) To tell the truth, the first 2 years I had symptoms (RA) I ate no night shades, sugar, gluten or coffee. I lost 50 lbs in 6 months but didn’t notice a dramatic decrease in pain. Does that mean I’m not that sensitive to night shades?, she asked with anticipation.

  2. I love this post! I was scared away from Paleo because of the AIP at first as well, so I started with GAPS instead (which is very similar to full Paleo). After 6 months, I improved, but then plateaued, so I was finally ready to try the AIP (and it made a huge difference). I don’t regret postponing it, though. Full GAPS/Paleo is a bi adjustment to begin with. Going from SAD to AIP would have been completely overwhelming. QuintEssentialOne, I have RA too and nightshades are a huge trigger for me. Wait until the winter and then give them all up for 30 days (including red pepper spices which are in almost every sauce, by the way, so you need to become a label reader). Be sure not to cheat at all, so they’re completely out of your system. Then reintroduce them and see how your body reacts. My body told me in no uncertain terms that they were inflammatory. I went from feeling great on AIP to feeling 90 years old overnight.

  3. I remember when Paleo was overwhelming! We started gluten free, then I did a Whole30 and THEN added in the AIP restrictions. Now it seems easy breesy!!

  4. Thank you for posting this. I am investigating Paleo because I have increasing issues with my digestive tract and practically everything I eat causes indigestion. But I also have MS and when I discovered that because of this I would ‘have’ to go on AIP, I could have cried. Seriously. Cried like a baby. I make great lentil soup which is loved by my family! And I love chickpeas and it’s going to be hard giving those things up without the added issues of the AIP too. So I will take it one step at a time and my first decision is to give up sugar. I know that’s not good for me already.

  5. The AIP is definitely overwhelming! Starting slow is the best thing to do. My daughter has health issues that are continually getting worse (we’re testing for celiac right now). When I first realized she may have celiac even the gfcf seemed like the end of the world. Then SCD? Too much to think about. Paleo was forget it! AIP is the worst. I couldn’t even imagine it. It ended with a lot of crying fits over what to feed my kid so she’d get better and how to even feed her on such restrictive diets. Now I’ve gotten use to the idea and it’s much easier. We’re still not going hard core enough for full AIP yet but we’re getting close! Only thing left that seems bad is honey, eggs, nuts and seeds (since we use these for paleo baking). I am hoping that this diet will help her and maybe we won’t even need to do anything further but I know now I’ll get there eventually even if we have to.

  6. I have decided to work towards paleo because of autoimmune issues. I was trying to do gluten free with a husband and 2 boys who can seemingly digest anything. It seems like it would be easier for me to eat paleo and round it out with their favorites stuff they can’t seem to do without. This way I don’t have to worry about all of those gf “flour” blends that produce less than ideal baked goods. My family has been real troopers so far. It is hard to change eating habits of loved ones after so long when they have no physical need for it. That is why I say working towards it, so hopefully I can change their habits eventually with great tasting paleo options and not get overwhelmed. The only thing I may never get them to do without is my homemade biscuits, but it is getting easier for me to leave them alone because I feel so much better with out wheat and dairy.

  7. Found your page looking for aip recipes. I’m freaking out for sure but I decided today I’m going full tilt. It’s going to suck for the first week as I detox from the sugar and caffeine but if I can make it one week, I know I can make it another and then another and then another. 30 days isn’t so long. I am already missing eggs and dairy but I’ve been sick for so long I’m tired of it all. I might fail. But I won’t know unless I try! And if I fail, i can just start over. I have to do this. But your article really did make me feel like I can do this. Because you are the first person to say “do what you can!” Instead of “you can’t go 90% or it won’t work!” You give hope to chronically bad eaters like me. :)

  8. I have a question; I just found out I have Graves disease and was looking to ways to treat it naturally. I had already been doing a ketogenic diet/lifestyle for a few months. One of the things I have read is that ketogenic diets are actually bad for autoimmune diseases, and they cause the autoimmune problems to worsen.

    I will say that I have been trying to follow an AIP diet for the past few weeks and I have noticed a huge difference in my symptoms (anxiety/tremors/palpitations) that have decreased exponentially. But I am concerned because I feel like I am eating way too many carbs (especially because I am eating fruit daily now). So I am thinking about a return to my ketogenic diet but not eating eggs/dairy/some nuts (which I think are triggers for me).

    Would you be able to confirm whether or not ketogenic diets aggravate autoimmune diseases? I am trying to weigh the pros and cons of staying on this AIP diet, which is very difficult even for someone who had taken out the grains and sugar etc. Thanks!

    1. Hi Rebecca,
      Thanks for your comment and I’m so sorry to hear about your recent diagnosis. Your question is a tough one to answer, because what aggravates a person’s autoimmune condition can be quite variable between individuals. In my experience, I have seen people have the most success at overcoming autoimmunity by following the AIP for several months (with the intention of healing their leaky gut syndrome). This may or may not restrict carbs, depending on how carb-sensitive the person is. After they are feeling better, many people can transition to strict Paleo or Primal and do great with it. I have found that I personally do best on a lower-carb, high-fat, Paleo diet (I have been diagnosed with multiple autoimmune disorders myself). But again, this is different for each person, and it does take some experimentation to figure out what will work best for you. Also just to let you know, I’ll be writing a blog article here on ‘Paleo and Graves disease’ in the next month or so. Please keep us posted on how you are doing, and let us know if we can be of any further help! I wish you all the best on your journey to wellness.

      Best regards,

  9. Start with 2 egg’s, Whole and raw, (like making egg nog only with the shells) mix with 2 cups ice and 2 bananas, for flavoring, this packs a morning and evening punch of calcium carbonate 1,000mg, with 27 micro nutrents for rapid blood transport, but the real winner is the Collagen types 1,3,4,5,10 in the egg shell’s membrane, heal’s everything it touches,and the collagen type 1 is same molecule as our’s, it shuts down autoimmune attacks in 90%, while it is missing collagen type 2 you can buy this easily, the other collagens in the egg’s shell membrane are all just as good and nessary and 1-5 makes up 95% of all our collagens, all in the eggs shell membrane, eating them raw, allows a cancellation effect of the egg white and you get full power dose of cholesterol, add 2 vitimane d-3’s and whamo, double sterol effect with auto immune shut down, and one last thing, virtually no one is allergic to raw eggs, its only when you cook them you change the molecular structures, you burn them up, and while you still get the protien you dont get effects from the collagens, good luck, I eat 6 a day without fail, and doing great, (one last point, research past Aug 2012, is pointless as FDA changed the entire egg packaging industry – Raw egg’s are safe now, so look at whole egg recalls currently in effect at lol none all sterial
    Good luck and good health and get well now ! Dan

    1. Hi Dan,
      Thanks for sharing your experience with raw eggs. Of course it’s important to note the source of the eggs, and that pasture eggs would be more preferable when consumed raw, as they are less likely to be contaminated with bacteria. Mark Sisson has some good thoughts on the topic of raw eggs. When attempting to heal a leaky gut and overcome autoimmunity, I would suggest completely removing all eggs from the diet for at least 6 weeks, and then conducting a provocation challenge.

      In good health,
      Kinsey Jackson, MS, CNS
      Paleo Plan

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