Autoimmune Disease

What is the Best Autoimmune Diet?

By Kim Crawford, M.D. Last updated: January 10, 2019
autoimmune diet


If you have been recently diagnosed with an autoimmune disease, please consider that leaky gut is usually the root cause of leaky gut.” Functional Medicine doctors address this cause whereas others don’t. If it isn’t addressed, no amount of dietary control—whether it is the autoimmune protocol diet, the autoimmune paleo diet or my “Crawford plan” autoimmune diet—will be enough to get you into a good remission. This article will focus on your eating plan and how to reintroduce foods into your diet.

The Autoimmune Protocol Diet

I often joke with new autoimmune patients that they’ll be joining me in “food prison”—I have Crohn’s disease. It actually is a big joke because when you get down to food basics, you will enjoy eating real food all of the time, and best of all, food will become your best medicine by helping you heal.

It’s going to be a choice between eating whatever you want, whenever you want, or feeling good. My “starter diet” is more strict than the typical autoimmune protocol diet because there are a few items in the typical diet which can be problematic. Here’s what the AIP diet includes (which I exclude).

  • Fruit (in small quantities); specific fruits are not specified.
  • Coconut milk; made popular by well-respected Functional Practitioners, Dr. Wahls and Dr. Meyers.
  • Dairy-free fermented foods, such as kombucha, kefir made with coconut milk, sauerkraut, and kimchi.
  • Honey or maple syrup (in small quantities).
  • Vinegar, such as apple cider and balsamic.

Dr. Kim’s Autoimmune Diet Recommendations

What Food Should You Eliminate? 

During the first two months, eliminate the following:

  • Refined sugars. This includes agave, maple syrup, and honey.
  • Processed foods and fast foods.
  • Dairy products.
  • Eggs.
  • Grains.
  • Seed oils, such as vegetable oils and canola oil.
  • Legumes, such as all beans, lentils, and peanuts. This includes hummus.
  • Nuts and seeds. This includes nut-based milk.
  • Herbs from seeds, like coriander, cumin, and nutmeg.
  • Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers, and okra.
  • Spices made from nightshades, such as chili powder, paprika, cayenne, chipotle, red pepper.
  • Dried fruits.
  • Alcoholic beverages.
  • Food additives such as gums and emulsifiers.
  • Coffee and chocolate.
  • Alternative sweeteners such as xylitol and mannitol with stevia being okay.
What Can You Eat? An Autoimmune Paleo Diet
  • All vegetables other than nightshades and white potatoes; sweet potatoes and other root vegetables are fine. Cruciferous veggies are also fine as long as they are cooked and not eaten in excess (even for Hashimoto’s thyroiditis patients). You can use flash-frozen organic vegetables too.
  • Poultry, fish, and meat; grass-fed, organic, wild-caught, humanely raised. Remember if the animal eats grains, so do you.
  • Small quantities of (low sugar) berries and a few fresh lemon/lime wedges.
  • All herbs which are not on the “elimination” list: basil, oregano, rosemary, dill, chives, cilantro, parsley, Italian parsley to name my personal favorites.
  • Oils for cooking: Healthy, high-flash-point oils (avocado, coconut, palm) and animal fats such as ghee and even duck fat.
  • For salads: Extra-virgin olive oil. Try salads with a squeeze of lemon, Himalayan sea salt and pepper.
  • Condiments: Vinegar; restrict to apple cider vinegar for two months.
  • Beverages: Loose organic herbal tea (hot or iced), bone broths (check the seasoning), water and unsweetened sparkling waters.
  • Stevia for sweetening.
autoimmune dietStarting Your Diet

For starters, clean out the pantry and fridge. Do a grocery shopping trip. Order products online. For example, ghee can be found online, as can many really interesting loose, organic teas.

You are not only on the path to feeling better, in (literally) about two weeks, but you’ll drop weight without trying. Indeed, cooking will become an easy task. You’ll have time to get very creative when your labs (e.g., CRP, ESR, Rheumatoid factor, TPO antibodies) normalize, and we advance your diet.

It takes at least a month to heal your gut lining. In month two, add probiotics to start normalizing the microbiome and also, herbals to clear up SIBO and SIFO. If you are healing your gut on your own, be sure to get good probiotics which will survive the trip through your stomach acid.

Why my Diet?

If you have an autoimmune disease, you have an unhealed leaky gut. The purpose of this diet is to remove anything that can cause food sensitivity and thus impede the healing of your gut. There is evidence that high FODMAP foods (such as coconut milk) are problematic for some people which is why I eliminate those particular items. We can quibble about the amount of coconut milk that qualifies as “high FODMAP” if you need a creamer for your tea. If you use less than 1/3 cup, you are probably okay, but if you have symptoms (usually GI), please discontinue it.

Vinegar can create IgG antibodies, too; if not apple cider. It’s the same scenario for honey and maple syrup. Fruit tends to be over consumed; even low-sugar fruit such as apples. So, leave these items off the list for now. During month one, your gut is leaky which means your gut-to-brain barrier is leaky.

As a result, we don’t introduce “fermented” foods until the middle of month two. The same FODMAP quantity caution applies to coconut milk when being used to make kefir. Fermented foods (which act as prebiotic fiber) can safely be introduced mid-month two or month three. During month two, also consume asparagus, plantains, onions and Jerusalem artichokes to serve as prebiotic fiber. Add a multi-fiber mix to leaky gut drinks for even more prebiotic fiber.

If you follow my list, drink a quality leaky gut mix, clear up SIBO and so on, by month three, you should be feeling significantly better, and when labs return as normal, it will be time to start cautiously advancing your diet. Note this diet is also great for those with heart disease, diabetes, nasal allergies and generalized inflammation. Also note that for those of you who are “strict AIP’er’s” that I allow more foods to be re-introduced. Consult your own doctor.

Food Sensitivity Testing 

Studies have looked at remission rates in those with, for example, Ulcerative Colitis, and found that IgG food sensitivity testing and food elimination based on that testing improved remission rates. The problem with food testing is that you must be actively consuming (within the last week or so) a specific food to create antibodies to it. On this basis alone, many foods “come up” negative, simply because you haven’t eaten them “lately.” When we reintroduce these foods to your diet, to check IgG antibodies, we’d need to add back potentially offending foods for a much longer period than I allow, or add back a whole lot of potentially offending foods and get you sick. Neither of these scenarios is ideal. I reserve food sensitivity testing for when we’re just not sure whether or not a certain food is causing you a problem; then we test.

The one area where you can “test” is looking for lectin sensitivity via genetic testing. While there is no specific test(s) to pinpoint lectin sensitivity, there are SNP’s which tend to be associated with lectin sensitivity. The more of these SNP’s you have, the more lectin-sensitive you are. If you are “very highly lectin sensitive,” you will probably need to avoid all of these lectin containing foods:

  • All grains.
  • Gluten from wheat, rye, barley, malt, and most oat products.
  • Nightshade vegetables: tomatoes, peppers, potatoes, and eggplant.
  • Chili, paprika, and cayenne pepper (derived from nightshades).
  • Legumes and all beans including soy and peanut. Cashews are also part of the bean family and not allowed.
  • Dairy, including milk and milk products such as cheese, cottage cheese, yogurt, and kefir. (With the exceptions discussed below).
  • Yeast (except brewer and nutritional).
  • Cucurbitaceae lectins, found in the rinds and seeds of cucumber, melon, and squash.
Eating More Creatively

Follow this diet, and you’ll start feeling better. If you have Hashi’s, you’ll likely have more energy, sleep well, and lose weight. If you have Crohn’s disease, those middle-of-the-night “trips” will cease. Further, if you have Rheumatoid Arthritis, you’ll get off Humira, and reduce “active” joint problems. You don’t want to “mess up” the positive results, but you may start craving eggs, coffee, or lentils, as one of my patients recently told me.

There are high-risk, moderate-risk and low-risk foods; Start with the lower risk foods or the food that you crave most in recipes. I recommend introducing one food every two weeks with a small quantity, careful observation, and occasional lab work. Go ahead and add your coffee if your gut is healed and your symptoms are gone.

An example of a low-risk food that has great utility is almond flour; as just 1/4 cup of it is used in a cauliflower pizza crust (recipe coming soon). Well-made nut flours tend to be “soaked”; meaning the lectins are soaked out of the nuts. The same goes for nut milk and when in doubt, it’s easy to make your own. Be aware nut milk is a high FODMAP in more than 1/3 cup quantities, so watch for GI side effects.

An example of a high “utility” low-to-moderate risk food is grass-fed pastured chicken eggs. Eggs are used in many recipes, and it’s hard to find a good substitute. Remember that “free range” is a garbage term—you need chickens that were fed only grass; not “grain-finished” chickens. The other good news (if chicken eggs are a problem) is that almost no one is sensitive to duck eggs, which can be found via local farms and the internet.


Beans (lectins), when soaked, might be okay for some people. If you are lucky, that may include even the pasta made from just beans and water. Soaked beans are a moderate risk; meaning you have over a 50% chance you’ll tolerate them. The highest lectin beans are kidney beans and if you’re going to experiment, look up the lectin content of what you’re going to try. There are two things you can do to reduce lectins in beans.

Soaking dry beans for two hours will yield a close to 1000-fold reduction in the lectin content of all beans. Then, if you pressure cook them (or use an Insta-pot), you will get rid of the majority of remaining lectins. Even highly lectin-sensitive people can eat some beans when prepared this way.


There is proven bio-mimicry of the gliadin part of gluten in most autoimmune diseases so forget about gluten. You might have read that there is less gluten in certain types of bread, but it’s still there. Even a speck of gluten will trigger all autoimmune diseases. I’m watching the development of gluten-dissolving oral enzymes; they are not where we need them to be, but I believe that an effective one is on the horizon.


While I am not a fan of eating a lot of grains in general (brain health, cardiac health, blood sugar control and more), the idea that all grains are out “forever” for all autoimmune patients might not be true. Lectin-containing grains have been blamed for flare-ups, but, in low-lectin-sensitive individuals, it may be due to the cross-contamination of gluten and non-gluten containing grains during storage.

However, I currently recommend avoiding grains except for sorghum and millet. Gluten-free sorghum is “safe” (not USDA gluten-free). To clarify, the term “gluten-free” means there is some gluten allowed by the USDA unless it’s a approved brand such as Bob’s RedMill—Bob’s makes a (gluten-free) sorghum “hearty bread” mix that even I can eat!

In addition, use coconut flour and/or almond or hazelnut flour to make bread, muffins, coating for chicken and fish, etc. Julian’s Bakery is an online source that uses these ingredients. also has great brands to explore products such as Siete’s grain-free tortilla chip (with a small amount of chia seed powder=caution for some) or sweet potato chips made in coconut oil. Blindly purchasing processed foods from un-verified sources labeled as “gluten-free” will likely contain unsafe grains, some gluten, and lots of sugar.

Nightshade Vegetables 

The lectins are found mainly in the seeds and the skins of all of these tasty vegetables. For a low-lectin-sensitive person (and some “moderates”) it might be safe to remove the skin and area with the seeds, and then pressure-cook these veggies. Try this with caution. At least you can liberalize your spices slowly; other than red pepper flakes, which will still be bothersome for all. For “low to moderates,” the Nomato brand products can be used in small quantities in lieu of tomato sauce, pizza sauce, and ketchup. However, if you can’t use these products, you can make a mean pesto sauce for most dishes begging for tomato sauce.


The mimicry problem with dairy is casein. Goat’s milk contains no casein, making all grass-fed goat’s milk products safe.

Now, let’s talk about cows. Have you heard of A1 versus A2 cows? Basically, it’s a genetic variant of cows, with most U.S. cows giving us A1 milk and some, giving us casein-modified A2 milk. Thus far, we know if you have certified A2 cows, they produce A2, casein-modified milk products. Always use organic, grass-fed A2 cow products. In addition, unpasteurized milk products contain more beneficial bacteria for your microbiome and many more nutrients. However, it’s more complicated than bio-mimicry so proceed with caution.

Consume A2 products in small quantities as all dairy will tend to spike your insulin a bit. Find Jersey-cow, grass-fed non-pasteurized (raw) cheese from Farmstead Fresh farms at I adore their Havarti cheese and eat it in very small quantities. Consider adding 3-4 organic raspberries. It is the perfect dessert! For pizza, find a minimally processed non-soy veggie cheese containing (safe) potato starch and tapioca starch.

Forget dairy milk and dairy coffee creamer. Why? Adding dairy to coffee nukes the healthy polyphenols in the coffee. Organic A2 butter and cream cheese are acceptable. For yogurt and kefir, stick to goat’s milk or coconut-derived. In fact, you can find some delicious coconut ice cream at

Although lectin-guru Dr. Steven Gundry allows A1 cream cheese and sour cream in his dietary recommendations, with the greatest of respect for his work; I am just not quite sure-so proceed with caution here.

“Safe” Nuts and Seeds

Pistachios, walnuts, almonds, pecans, hazelnuts, and macadamia nuts are safe. Peanuts, soy, and cashews (all “beans”) are not. Hemp seeds are safe. Chia seeds are an “individual thing.” Unlike true allergic reactions (IgE-based) sensitivity to this and other foods might be “dose-dependent” so always keep that in mind. Other seeds, even raw, sprouted, and so on, are generally not safe.


Most people can add balsamic vinegar and even (unless you are highly lectin sensitive) dill pickles. If you can eat eggs, you can make your own mayo or use Primal Kitchen mayo in small quantities. Nomato ketchup is usually safe in small quantities, as is organic mustard. Sprinkle nutritional yeast flakes for a cheesy Parmesan substitute. If you have room on your porch, it’s easy to grow fresh herbs such as basil and cilantro in clay pots. Coconut flakes and even raisins or small pieces of dried prunes also make for interesting additions to salads.

Odds n’ Ends

Cricket flour is a new form of protein that appears to be safe to use in recipes instead of conventional flours. If you’re looking for a protein powder, hemp protein powder (organic, non-GMO) is available on Organic, non-GMO corn and non-microwave popcorn are safe, in reasonable quantities for most people. (The reason for intolerance is that it’s a common IgG food sensitivity item for those with autoimmune diseases.)

You can make muffins and cookies with substitute flours and stevia or erythritol. You can also make baked apples with stevia and cinnamon and top it with whipped coconut cream. Most of us can eat up to four squares of organic dark chocolate daily. You can always grate this on top of your coconut cream topping, too! Acceptable low-sugar alcohol is champagne, red wine, and white spirits. A splash of cranberry juice in vodka is okay (as it happens to be the lowest sugar juice).

During the end of month two you can add back your coffee and add 1 TBSP of sugar and additive free almond milk, plus 1 TBSP of sugar and additive free coconut milk. Finally, find social media recipe groups and even disease support groups for inspiration. I belong to a gluten, dairy and soy free recipe group that is great!

Lastly, remember to supplement your vitamin D, and use a superb multivitamin with the right fish oil blend.

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