Planning for the Autoimmune Protocol


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9 thoughts on “Planning for the Autoimmune Protocol

  1. I am so glad this blog exists now. I’d love to hear what some people have experienced with this diet, as I am quite new to it. I’ve eliminated dairy, legumes, and most grains, but I haven’t reached my health goals. How long I should do the protocol for? I guess it’s different for everybody, but what is a reasonable amount of time to do the strict diet?

    Also, have any of you struggled in social situations with explanations of your new diet? I’ve been faced with some upsetting responses from friends who think this is the wrong way to address my health problems. Any tips with this would be great.

  2. Hi Kaitlyn,
    I think at the very minimum, to use the autoimmune protocol as a strict elimination diet for 30-60 days and then begin to introduce foods one at a time, a few days apart to really get a chance to see how they make you feel. It sounds like you are on a paleo type diet, which is a great start. I would suggest that if you have any sort of autoimmune disease you look into eliminating all grains, even the non- gluten ones.

    As for social situations, they are very tough. I have not yet mastered how to integrate the autoimmune protocol into my social life without looking like a crazy person. Most of the people in my life are understanding enough to bear with me as I tote my own food around wherever I go. I am planning some posts on this topic in the future.

    And as for your friends – I think they are right in being concerned with your plan to treat your problems with diet. You should always consult a doctor first regarding your health problems. I believe diet change can have a profound impact on autoimmune disease, but it would not be wise to embark on a plan without consulting your medical provider.

    Thanks for your questions!

  3. Mickey – With cutting out nightshades, and goitrogenic (cruciferous veges) what type of veges are left and so you don’t repeat the same ones over and over again? I feel so overwhelmed again and not sure which veges to use. Are raw salads ok with cooked meat and cooked veges too? It is so darn frustrating to have to limit the good for you foods (like veges and fruits) – somehow does not seem “fair”… Anyway… just wanting to fill up on veges and not as much meat as I was eating, plus some fat, plus keeping in line with elimination AI protocol and nightshade and goitrogenic concerns. Oh brother! LOL

    • Christina,
      I wouldn’t worry about the goitrogenic vegetables unless you have pinpointed them as a problem for you. I know there are a lot of websites hyping that they are a big deal for thyroid, but I haven’t seen much evidence that their effect is more than minimal. I eat lots of the following: winter squash (delicata, spaghetti, butternut, acorn), lettuce, carrots, celery, cucumber, chard, arugula, radishes, green beans, bok choi, parsnips, and olives. I also eat these in small amounts (because of sibo): kale, collards, broccoli, brussels, cabbage, beets, sweet potatoes, yams, cauliflower, turnips, celeriac, rutabaga, and jicama. Raw salads and meat are great. I wouldn’t steer clear of raw food unless you notice that it causes you digestive upset. Winter squash is a great vehicle for fat – I eat a serving with 2-3 tablespoons of coconut oil and it is really satiating.

      Hope it helps!


      • Thank you it helps alot. It is so hard to tell what is giving me issues. Everything I eat, I swear, gives me “gas”. Even just drinking a cup of bone broth does! Oh brother! I feel like I am feeding a SIBO condition, but I don’t want to keep taking things out because I lost too much weight last year from malabsorption syndrome. Now even if I eat too much squashes (which I love) to keep the weight on, my skin turns yellow! Oh vay! 🙂

      • I hear ya! I have learned to live with some of the symptoms in favor of variety in my diet. I am not sensitive to the beta-carotene in squash but my husband is – if we eat it too often he looks like a pumpkin 🙂

      • May I ask what you do to remediate the skin coloring? I know to back down, but it is hard to avoid those delicious gifts at this time of the year. Also, greens have beta carotene too, not just the orange veges. Thanks!

  4. Thank you so much for this site. I suffered from Glandular Fever (Mono) 2 years ago and have been dealing with fatigue ever since. I also found out in December that I have hypothyroidism (for which i am on medication) and have suffered my entire life with psoriasis. I stated following a regular paleo diet at the start of Feb this year and have seen amazing results with my weight dropping from 65kgs to 57kgs (not sure the lb equivelant, sorry!) in these last few months, with no heavy exercising. The health is still a problem though. I am going to get started on this protocol very soon but just waiting for a couple of events to pass which I know will be problamatic to stick to it. In the meantime i have cut outs eggs, buts, seeds and nightshades comepletly and cut down on coffee (and the milk that goes in it) and alcohol. Anyway, I havent eaten a nightshade in 4 days and accidently ordered some roasted pepper in my salad today for lunch as i must have been on autopilot. I didnt realise until i had finished the whole salad! Almost immediately i was overcome with bloating and cramping in my stomach. About an hour later was rushing to the bathroom, had an acute headache and my glands had swollen (which is an indicator that fatigue is coming or here already). Now, an hour after that the fatigue and headache are still unrelenting. It is amazing the effect one little pepper has had on my body. I love them so much that it was always going to be one of the hardest things for me to give up… bye bye bolognaise sauce *sniff*. Now I can feel first hand what it does to my body and i never want to go down that road again – and i haven’t even properly started the cleanse!
    Anyway, sorry for the long-winded email. If you have any further recommendations then would love to hear it. Am going to buy some FCLO as soon as I can and ditch the other supplements. Hopefully i can ditch the thyroid medication as well soon but have yet to go back for tests.

    • Hey Bec! Glad you found me here, although my blog has moved – I am now at That is why it has taken me so long to get to your comment!

      I think the autoimmune protocol would be a great idea for you, and wow, that is crazy how you could tell your reaction to nightshades after only four days! I also have a bad reaction to them. I have been able to reintroduce a lot of my favorites (nuts, seeds, eggs) but I think nightshades will be off the list for a long time.

      My further advice would just be to take it slow, be gentle on yourself, and enjoy your healing process. It is empowering to take your health into your own hands. 🙂


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