Reintroducing Foods after Following the Autoimmune Protocol

September 13, 2012 in Categories: , by

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The paleo diet autoimmune protocol is an elimination diet designed to reduce inflammation, decrease production of autoantibodies and heal the gut.  The most expedient way to see improvement is to follow the autoimmune protocol very strictly at least for a month (although there are other options, discussed in this post).  Most people will see some improvement in their symptoms over that time (those that do not see noticeable improvement may wish to consider food sensitivity testing and also watch out for foods with a high likelihood of gluten cross-reactivity).  Many people are then eager to start reintroducing the restricted foods.  This post is designed to guide you through that process.

So, first, let’s talk about how you will know that you are ready to start reintroducing some foods.  I suggest waiting until you see improvement in the symptoms of your disease (this will be highly individual).  You should see at least some improvement in your symptoms within one month of following the autoimmune protocol (for some, it may take as long as three months to notice improvement).  As you continue to follow the autoimmune protocol, you should continue to see improvement, although it may be slow (see this post for why) and some people may not experience full remission of their disease until they have followed the autoimmune protocol strictly for many months or even several years.  Unfortunately for some, permanent damage may mean that a full recovery is not possible.  In the case of aggressive and destructive autoimmune diseases, the autoimmune protocol will still help slow and perhaps halt the progression of the disease, even if meaningful improvement is not possible.

It is your choice whether to wait until you see some improvement of your symptoms or to wait until you have fully healed before reintroducing restricted foods.  How you feel is the best gauge and only you will know if you are ready.  A word of caution though:  don’t let missing foods drive this decision; it really should come from feeling good and seeing improvement in your disease.

If you have been following the autoimmune protocol strictly for a period of months without improvement, there are two options.  You may need to follow additional vegetable restrictions (see this post on FODMAPs and this post on SIBO).  I also suggest considering food sensitivity testing as you may be continuing to consume a food to which you are sensitive.  You may find the book Practical Paleo a tremendous resource because Diane Sanfilippo outlines a variety of supplements which can help speed healing for those with leaky gut and autoimmune disease.  I have also invited a number of alternative healthcare professionals to provide their take on the benefits of the services they provide (naturopathic physicians, chiropractors, acupuncturists, and physical therapists), which may be a good option for you.  And of course, working with a food-savvy medical professional can also be exceedingly helpful.

Once you have decided to reintroduce foods, I suggest reintroducing from least likely to cause issues to most likely (I’ll order the foods below).  When you reintroduce a food, consume only a small amount of that food, at least twice on two consecutive days.  Reintroduce one food at a time, giving at least 3 days in between reintroduction before trying the next one (this is even true for seed-based spices).   If you have a violent reaction to a food, you will have to wait a couple of weeks for your immune system to calm down before reintroducing the next food.

What should you look for to determine if you can continue to consume this food? Even one of the following symptoms is enough to stop eating that food.  You can always try again later in case the symptom was a coincidence.  Also, even if you cannot tolerate that food now, as your body continues to heal, you may be able to in a couple of months.  Symptoms to watch for:

  • Any symptoms of your disease returning or worsening
  • Any gastrointestinal symptoms:  tummy ache, changes in bowel habits, heartburn, nausea, constipation, diarrhea, gas, bloating, undigested/partially digested food particles in stool
  • Reduced energy or fatigue
  • Strong food cravings: sugar cravings, fat cravings, pica (mineral cravings)
  • Trouble sleeping: either falling asleep or staying asleep or just not feeling as rested in the morning
  • Headaches or dizziness
  • Aches and pains: muscle, join, or tendon/ligament
  • Changes in your skin: rashes, acne, dry skin, little pink bumps or spots; dry hair or nails
  • Mood issues:  feeling low or depressed, having a lower ability to handle stressful situations, increased anxiety

What order should restricted foods be reintroduced?  I have classified foods from lowest to highest likelihood to be problematic.  Start with the lowest and work your way up.  Within each category, just pick the food that you miss the most.  If you have had food sensitivity testing done, leave any foods you have a diagnosed sensitivity for last (or perhaps before nightshades).

Least likely to be problematic:

  • Egg yolk (if you don’t tolerate them, make sure you are buying pastured, soy-free, wheat-free eggs and try again)
  • Ghee from grass-fed dairy
  • Seed-based spices (as long as they aren’t nightshades)
  • FODMAP foods if you have been avoiding them (this sensitivity should greatly diminish or go away completely when your gut has healed)
  • Salicylate or High Histamine foods if you have been avoiding them (these sensitivities should go away when your gut has healed)

The next least likely to be problematic:

Moderately likely to be problematic:

Most likely to be problematic:

You may never want to consume:

I have successfully reintroduced egg yolks, seeds, and nuts except almonds, grass-fed butter, cocoa, and starchy vegetables (as long as I keep the dose of all of these things low).  I understand well how reintroducing just these few foods can feel like a huge improvement to my quality of life.  I hope that you also find at least some foods that can be successfully reintroduced!  Good luck!


I was curious if the coffee addition being likely problematic stems from the fact that it’s a seed or the caffeine?

My Endo told me that the caffeine is problematic, but I can see the bean issue as well. I recently reintroduced coffee. I still don’t eat any dairy, so I use almond milk in it. I only drink it on occasion, though.

I’ve read your recommendations and procedures for reintroducing foods but have a question. How do you take a nibble of a spice? With spices do you just use them once or twice in a day and then follow the protocol of doing nothing for 3-7 days while monitoring how you feel? Or do you have a different recommendation? Thank you so much for all you do. John

I have a scalp/hair condition that has an autoimmune component. If food bothers me I cannot tell. I have had a basic food allergy test done at the doctor. Nothing turned up. I have been on the autoimmune paleo diet, strict, for 7 weeks. I see no improvement in the condition, and I feel no different, no better, no worse. (Except I feel more hungry than usual…) I felt fine before. I am also taking a probiotic, multi-vitamin, biotin and now keratin, plus fish oil. My motivation to reintroduce foods prior to symptom relief is the fact that I am throwing a party and I want to enjoy myself, eat the appetizers and have a beer. Is there some science that proves that all autoimmune diseases can be linked to the gut? My motivation to try the diet is there is no cure or known effective treatment and the consequence is permanent scarring and loss. It is all such a mystery…

Hi! I have Grave’s disease which is now in remission! :) I had hair loss issues and it did not stop until my thyroid stimulating hormone was in the normal range. I take biotin and use a biotin shampoo to improve my hair growth. I do not eat beans, dairy, or wheat. (No beer,,,but try Greens…it’s gluten-free) I eat predominately vegetables and fruits as well as fish, chicken, and deer in small amounts. I am sorry that your condition is not improving, but you might want to see if you have a coexisting autoimmune disease as they, too, can cause hair issues. Hashimotos, lupus, psoriasis and a few others also cause scalp issues. Also, try diluted tea tree oil and eat more coconut products to see if that helps! All the best to you!

I have been on the AIP for almost a year, and have just killed off my SIBO about two rounds of herbals (yay!). During the food reintroduction process, any tips for mitigating the symptoms when you do have a bad reaction? I get tired, spacey, headaches- it makes it hard to concentrate at work. Cardio and L-glutamine supplements are helping a bit, but any other suggestions? Thanks so much!

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