What Are The Best Diets For Autoimmune Disease? (GAPS, Autoimmune Procotol, LowFODMAP & more)

Autoimmune diseases can affect nearly every part of the body. Scientists have identified more than 80 clinically distinct autoimmune diseases, including systemic lupus erythematosus, type 1 diabetes, rheumatoid arthritis, Sjögren’s syndrome, multiple sclerosis, and chronic inflammatory bowel disease.

Having an autoimmune disease means you're probably dealing with symptoms that could range from mild or severe. Often you're left with many persisting symptoms, despite treatment that may leave you curious about your other options for controlling your disease. In this article I'm going to do an extensive overview of many of the diets that have been associated with improving the health of those with an autoimmune disease. Using quality nourishing nutrition to manage autoimmunity can help control pain and reduce inflammation. While diet is not going to cure your condition, it can help improve your overall health and reduce symptoms.

Unfortunately many of these diets are only supported by anecdotal evidence, meaning it's based on people's experiences and not actual scientific proof. That being said these diets are nutritionally dense and a far improvement from the standard American diet. Many have reported large improvements in their health following the diets below.

Autoimmune Protocol (Autoimmune Paleo)

What is it?
The Autoimmune Protocol is an extensive elimination and reintroduction diet with a paleo template. The diet removes foods considered to be gut irritants like grains, legumes, dairy, eggs, gluten, seeds, nuts, sugar, alcohol, refined oils, and processed foods for a period of at least 30 days. By reducing gut irritants and removing potential food sensitivities then replacing them with nourishing foods you can support gut health and lower inflammation.  

AIP was originally constructed by Dr. Loren Cordain who made a link between certain foods triggering inflammation in those with autoimmune conditions. Later Sarah Ballantyne (thepaleomom) PhD was attracted to to AIP through her own research and has become the leading expert in this diet. She wrote a book called The Paleo Approach where she covers everything you need to know about the autoimmune protocol. For at least the first thirty days you eliminate grains, eggs, gluten, legumes, dairy, seeds, nuts, sugar, alcohol, refined oils and processed foods. After 30 days or when you start to see feel relief of your symptoms you can start re-introductions. Some foods are to be eliminated permanently like gluten, grains, processed foods, emulsifiers and thickeners (guar gum, carrageenan, etc.), refined oils, refined sugars and dried legumes (including soy and peanuts). Other can be slowly reintroduced one at a time to see if there is a reaction.

Beyond Diet: The AIP protocol is more then just diet even though that's the main focus. Reducing stress, getting proper sleep, and reducing toxins is all part of the protocol.

What's eliminated?

  • Grains - wheat, rice, corn, and others; (millet, amaranth, teff, etc.)
  • Legumes – all beans including peanuts, black beans, pinto beans, hummus, etc.
  • Dairy – all sources of dairy, even raw or fermented
  • Nuts and seeds - all nuts and seeds including cashews, almonds, quinoa, sunflower seeds, sesame seeds, seed-based spices, chocolate, coffee, etc.
  • Eggs - especially the white part of the egg, which contains inflammatory proteins
  • Nightshades - tomatoes, potatoes, peppers, eggplants, goji berries and several spices
  • Industrial seed oils - pretty much all liquid oils, except for olive and avocado oils

What's Allowed?

  • Vegetables of all kinds and colours (except nightshades
  • Good quality seafood, particularly fatty fish rich in omega-3 fats.
  • Quality meats, especially organ cuts (offal) such as liver.
  • Quality fats such as extra virgin olive oil, avocado, coconut oil (to a lesser extent).
  • Fermented foods (probiotic sources) such as kefir, pickled vegetables, sauerkraut, kimchi.
  • Fruit in small quantities.

Who's it for?
Autoimmune protocol is for individuals who continually struggle to manage the symptoms of their autoimmune condition. But there are several important reasons not to try an AIP diet like numerous medical conditions, disordered eating and those who don't have an autoimmune condition.

Wahls Protocol

What is it?
The Wahls Protocol was created by Dr. Terry Wahls whose personal struggle with progressive ms resulted in life in a wheelchair. Even though Dr Wahls had access to the very best care and drug treatments available, she continued to deteriorate. She was told that any function lost as the disease progressed would never return. By 2003 Dr Wahls needed a cane to walk and shortly after needed a wheelchair. At this point she started researching why her body was failing and what she could do about it. She had already been on a Paleo diet but was still declining. After discovering some food intolerances she went on a more strict version of paleo. She highly increased her vegetable intake and also increased her intake of B vitamins, co-enzyme Q, antioxidants, and organic sulphur. She managed to reduce her symptoms enough where she no longer needs a wheelchair.

The Wahls Protocol emphasizes nutrient dense foods and lots of vegetables (up to 9 cups a day!). There are three levels of the Wahls Protocol, each one more strict then the last. The three levels are discussed below:

What's eliminated? 

Level 1 Wahls Diet This is the entry-level program for those transitioning from a typical American diet. The restrictions are no gluten, no eggs, no dairy (with the exception of ghee), no refined oils, limited sugar and no processed foods. The focus is nutrient density: she asks you to ramp up to 9 cups of vegetables daily (3 cups greens, 3 cups sulfur-rich, and 3 cups colorful). Eating organic grass fed meats are important.

Level 2 – Wahls Paleo You start with the details of the Wahls Diet listed above and add the following elements: (1) Reduce consumption of non-gluten grains, white potatoes, and legumes to only twice per week and remove soy altogether (with the exception of fermented soy). (2) Increase meat consumption to a minimum of 9 ounces daily. (3) Increase your healing foods to include organ meats, seaweed, fermented foods, soaked nuts/seeds, and more raw foods.

Level 3- Wahls Paleo Plus This level is a ketogenic diet (high fat, low-carb and moderate protein), but unlike conventional ketogenic diets, it is specifically designed to include 6 cups of vegetables daily for nutrient density, while still maintaining ketosis through the chemistry of eating 5 tablespoons of coconut oil per day. It’s also stricter than the prior Wahls levels. It requires 100% compliance, eliminating all grains, legumes, soy and white potatoes, and limiting starchy vegetables to two servings per week and fruit to 1 cup of berries daily. Protein is reduced according to size and gender, with the emphasis of shifting the body to burning fat for energy.

What's Allowed?

  • 3 cups of green leafy vegetables (daily)
  • 3 cups of sulphur rich vegetables (daily)
  • 3 cups of bright colour (peppers, berries, fruit) (daily)
  • Grass fed meat (several times per week)
  • Wild seafood (several times per week)
  • Seaweed (at least once a week)

Who's It For?
While the Wahls Protocol is directed towards people with multiple sclerosis, it's mentioned in the book that anyone with autoimmune disease can benefit.

GAPS (Gaps and Physiology Syndrome) 

What is it?

GAPS stands for the Gut And Psychology Syndrome. It makes a connection between the health of the digestive tract (permeability, balance of microbes, inflammation, etc.) and the health of the nervous system and the rest of the body. GAPS was developed by Dr. Natasha Campbell-McBride, a medical doctor and neurologist, with a masters in nutrition.  She outlines the diet in detail in her book Gut and Psychology Syndrome.

GAPS is a three part protocol which includes:

  1. Therapeutic diet
  2. Supplementation
  3. Detoxification therapies

The dietary component of GAPS is based on the Specific Carbohydrate Diet diet (SCD). The GAPS diet focuses on healing and sealing the gut lining by removing all food stressors for an extended time, and treating with foods like bone broths, as well as helping the gut flora rebalance with fermented foods and probiotics.

Typically one who is serious about the GAPS Protocol goes through the 6 stage Introduction Diet first (usually 3 – 4 weeks) and then moves on to the Full GAPS Diet for 18 months to 2 years. This allows the body to gradually and safely re balance and replenish nutrient stores while at the same time detoxifying and repairing damage.

What's eliminated?

  • Processed foods
  • All Grains
  • Processed sugar
  • Starchy carbs and potatoes
  • Artificial chemicals and preservatives
  • Conventional meat and dairy

What's Allowed?

Full List & Stages

Who's It For?
The GAPS diet is claims to treat Crohn's disease, ulcerative colitis, diverticulitis, celiac disease, cystic fibrosis, chronic diarrhea. It has also been used by others with autoimmune disease.


What is it?
The low-FODMAP diet was developed at Monash University in Melbourne, Australia in the late 1990s and early 2000s. Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols or (FODMAPS) are carbohydrates that are not absorbed in the small intestine and may pass into the large intestine where bacteria ferment them, resulting in bloating and gas. This occurs in many individuals and does not cause significant issues for them, but for others it results in symptoms of IBS including abdominal pain, nausea, diarrhea and/or constipation, flatulence and other gastrointestinal symptoms. It is not exactly clear why FODMAPs bother some people with the inflammatory bowel diseases (IBD), but pilot studies have shown that following a low-FODMAP diet does help reduce symptoms in people with active Crohn’s disease.

What's eliminated?

  • Excess Fructose: Honey, Apples, Mango, Pear, Watermelon, High Fructose Corn Syrup,
  • Fructans: Artichokes (Globe), Artichokes(Jerusalem), Garlic (in large amounts), Leek, Onion (brown, white, Spanish, onion powder), Spring Onion (white part), Shallots, Wheat (in large amounts), Rye (in large amounts), Barley (in large amounts), Inulin, Fructo-oligosaccharides.
  • Lactose: Milk, icecream, custard, dairy desserts, condensed and evaporated milk, milk powder, yoghurt, soft unripened cheeses (eg. ricotta, cottage, cream, marscarpone).
  • Galacto-Oligosaccharides (GOS): Legume beans (eg. baked beans, kidney beans, bortolotti beans), Lentils, Chickpeas
  • Polyols: Apples, Apricots, Avocado, Cherries, Nectarines, Pears, Plums, Prunes, Mushrooms, sorbitol (420), mannitol (421), xylitol (967), maltitol (965) and isomalt (953).

What's Allowed?

  • Vegetables- Alfalfa, bean sprouts, green beans, bok choy, capsicum (bell pepper), carrot, chives, fresh herbs, choy sum, cucumber, lettuce, tomato, zucchini.
  • Fruit- Banana, orange, mandarin, grapes, melon
  • Lactose-free milk, lactose-free yoghurts, hard cheese
  • Meats, fish, chicken
  • Grains- Gluten-free bread and sourdough spelt bread,  oats, gluten-free pasta, rice, quinoa
  • Nuts & Seeds- Almonds (<10 nuts), pumpkin seeds

Who's It For?
There was effectiveness in treating functional symptoms in inflammatory bowel disease from small studies (2). There has also been some evidence that it helps with IBS.(3)

Specific Carbohydrate Diet (SDC Diet)

What is it?
The SCD was first described by Dr Sidney Haas in 1924 as a way to treat celiac disease. The SCD was popularized for the treatment of IBD by biochemist Elaine Gottschall through her book Breaking the Vicious Cycle after her daughter was daughter found relief of ulcerative colitis using the diet. This diet is based on the theory that disaccharides and polysaccharides pass undigested into the colon, resulting in bacterial and yeast overgrowth, which causes overproduction of mucus. The concept continues to state when complex carbohydrates are poorly absorbed during digestion, they act as food for the harmful bacteria in our intestines. This can result in bacterial overgrowth, which can cause inflammation of the intestinal wall. The SCD diet is meant to starve these bacteria by eliminating complex carbohydrates from the diet for several years and restoring the balance of bacteria in our gut.

What's eliminated?

  • Sugars: lactose, sucrose, high-fructose corn syrup, fructose, molasses, maltose, isomaltose, fructooligosaccharides, and any processed sugar
  • All canned vegetables
  • All grains: anything made from corn, wheat, wheat germ, barley, oats, rye, rice, buckwheat, soy, spelt, and amaranth
  • Some legumes: chickpeas, bean sprouts, soybeans, mung beans, fava beans, and garbanzo beans
  • Starchy vegetables: potatoes, yam, parsnips, seaweed products, agar, and carrageenan
  • Canned and processed meats
  • Dairy: milk, milk products, ice cream, whey powder, commercial yogurt, heavy cream, buttermilk, sour cream, and the following cheeses: ricotta, mozzarella, cottage cheese, cream cheese, feta, processed cheeses, and cheese spreads
  • Canola oil, commercial mayonnaise, commercial ketchup, margarine, baking powder, and balsamic vinegar
  • Candy, chocolate, carob

What's Allowed?

  •  Vegetables (except canned)
  • Legumes (except the ones noted below)
  • Unprocessed meats, poultry, fish, and eggs
  • Natural cheeses
  • Homemade yogurt fermented at least 24 hours
  • Most fruits and juices without additives
  • Nuts, peanuts in the shell, natural peanut butter
  • Oils: olive, coconut, soybean, and corn
  • Weak tea and coffee
  • Unflavored gelatin
  • Mustard and vinegar
  • Saccharin

Who's it for?
SCD claims to people with various forms of bowel disease (Crohn’s disease, ulcerative colitis, celiac disease, diverticulitis, cystic fibrosis and chronic diarrhea).

Plant Based Diet

What is it?
A plant based diet is based on fruits, vegetables, tubers, whole grains, and legumes; and it excludes or minimizes meat (including chicken and fish), dairy products, and eggs, as well as highly refined foods like bleached flour, refined sugar, and oil. It focuses on reducing inflammation through out the body. A whole, plant-based foods means more antioxidants, more nutrients, vitamins, minerals, and more fiber.

What's Eliminated?

  • Meats (minimized or eliminated)
  • Dairy (minimized or eliminated)
  • Eggs (minimized or eliminated)
  • Sugar
  • Bleached Flour
  • Oil

What's Allowed?

  • Fruits
  • Vegetables
  • Whole Grains
  • Legumes

    Who's it for?
    While this diet can be controversial in the autoimmune nutrition world where a more of a paleo diet has become popular, many people have seen the benefits of the anti inflammatory nature of this diet.

Which one works for me?
Feel like your head is spinning? I don't blame you! Trying to figure what dietary changes to make is overwhelming. There seems to be a for and against for almost every diet and food out there. My best advice is do your research, don't let it stress you out and plan plan plan. Remember a diet that works for someone else may not work for you. Everyone is biochemically different, meaning that we all have different nutritional needs. A good place to start is with an elimination diet because that way you can figure out which foods react with your body. You want to learn all about what works for you and makes you feel your best. That's the end goal, to have created a custom diet where you are feeling your best. Everyone can benefit from increasing your vegetable intake and reducing (ideally eliminating) your refined sugar, unhealthy fats and processed foods intake.

Many people with autoimmune conditions have found relief using other diets like a vegan diet or a Mediterranean diet. Though I didn't mention them above that doesn't mean they are poor diets for those suffering autoimmune conditions. If you are eating healthy and feeling well then keep doing what you're doing!

 Before Starting a New Diet

1. Research- Don't just jump in without planning (research recipes, learn the ins and outs, be realistic). Also, don't start during a stressful time because that's just setting you up to cave and go back to old habits.

2. Get Support- Talk to your doctor and health care team before starting any new diet. Consider hiring a nutritionist to get one on one guidance.

3. Be Careful- It's easy to misuse these diets and end up with nutritional deficiencies. Before you start cutting out food groups make sure you know what nutrients you'll need to replace. 

Beyond Diet:
While changing your diet is a big piece of the puzzle to feeling better, there are other factors that are really important. Lifestyle factors like high stress, a high toxic burden, lack of exercise and infections (like SIBO, parasites, dysbiosis) can all affect your health. Looking at your health from a whole perspective gives you the best change at feeling your best.

Have you tried any dietary changes to help reduce autoimmune symptoms?