A Deep Dive into Diets
Comparing Autoimmunity Suggested Diets

In the world of autoimmune disease, diet stands at the front lines of tackling uncomfortable symptoms. In this article, DrBonnie360 breaks down some popular diets that have more implications beyond the hype of trendy culture.

As many of you know, I suffer from a plethora of autoimmune symptoms. Over the years, I have been to countless doctors, received numerous diagnoses, and pressed on to fight this battle with autoimmune disease. Although I haven’t found my “optimal diet”, one thing is clear to me: food does matter. Even though I specialized in nutrition during dental school, navigating this new world of autoimmunity, nutrition, and diets has been a complicated process.

I went gluten-free over 10 years ago, and about 3 years ago went dairy-free and reduced my sugar intake. These three diet modifications seem to be pretty standard starting points in the world of autoimmunity. But are they enough? Too much? Are these modifications actually best for everyone in a world where we continue to discover our uniqueness? Do we even know the difference between these autoimmune specific diets? Why they work, when they work? Clearly, there are around a billion questions to unpack, and we did a bit of digging to find some answers.

Autoimmune Specific Diets

The gradual rise of autoimmune and other inflammatory diseases over the last century means they now affect some 50 million Americans; the focus on nutrition and diet to mediate these symptoms, however, has only gained traction within the last decade.

Gluten Free

This diet is probably the easiest to understand and has become increasingly easy to implement. Gluten is a protein found in wheat, barley, and rye grains and is prized for its ability to help leavened bread rise. It’s pretty common in European diets of both the Mediterranean and the North, as well as North China, North India, Central Asia, the Middle East, and other countries settled by people from these cultures (1).

I know what you’re thinking: with such wide-spread use of gluten, how did the idea of gluten-free diets even start? It turns out that there was a huge decrease of wheat production in WWII, resulting in severe shortages of the daily staple. Interestingly enough, Dutch pediatrician, Dr. Willem-Karel Dicke, found that the frequency of celiac disease plummeted during the war and rose again after the war ended. This was the first clue linking celiac disease to gluten (2). In the 1940’s and 50’s, further research found that a diet without gluten resulted in complete remission of celiac patients (3). With an increase in awareness, gluten-free has become fundamental in helping people diagnosed with celiac.

Discerning the hype

Recently, the gluten-free diet has spread far beyond diagnosed celiac patients and has become a popular and over-hyped fad diet today. Gluten-free foods now flood grocery stores and are even available in many restaurants. Of course, in light of all the hype, the increased accessibility makes this diet one of the easiest to implement.

If you couldn’t tell from its name, this diet simply removes the gluten from your diet. This means avoiding all foods containing any wheat, barley or rye ingredients. That can be tough, as gluten naturally occurs in most breads, cereals, and processed foods. Luckily, there are many non-gluten grains and starch substitutes that you can eat. These include rice, quinoa, potato, soy, oats, tapioca, coconut, and others. The bright side of the fad is that gluten-free alternatives are widely available and clearly labeled. The darker side includes some over-promoted, overpriced specialty foods and the practice of labeling obviously non-grain foods (meat, vegetables, soda, water) as gluten-free.

What’s on the table?

  • On the table: All fruits, vegetables, beans, seeds, eggs, meats, fish/shellfish, poultry and dairy products
  • Off the table: Gluten protein: wheat, barley, rye breads and cereals, processed foods with gluten added (means reading labels or asking waiters)
  • Best for: Celiac patients, recommended for IBD, IBS and Crohn’s disease, worth checking out for other intestinal sensitivities
  • Read more about it: diet outline
  • Meal plans & recipes: Celiac.org, Allrecipes, FoodNetwork
  • Meal kits & delivery services: HelloFresh-gluten free, SunBasket, GreenChef


Paleo is the popular nickname for the Paleolithic Diet, which is based on following a diet more like that of our pre-agricultural ancestors (think cavemen in the Stone Age). The Paleolithic era long precedes the Neolithic period, when Homo sapiens first began farming some 10-14,000 years ago (4,5).This agricultural revolution enabled civilization: towns and cities, key precursors to modern life, which still today relies on grains for most of peoples’ calories (see gluten-free above).

The Paleo diet builds on the idea that for hundreds of thousands of years, our ancestors hunted meat and gathered nuts and fruits rather than planted and harvested grains and legumes (4,5). Therefore, our genes may not have caught up with the dietary change, and, as a result, food sensitivities to agricultural products are more common in the population. Some Paleo dieters also avoid dairy. This practice is founded on the grounds that while animal domestication gave rise to the practice of eating meat, consuming milk and milk products is a more recent development dependent on the emergence of adult lactose tolerance in two populations less than 10,000 years ago.

Motivations for paleo dieters vary. Some avoid grain proteins (like gluten) that are suspected to trigger sensitivity reactions. Others believe that grain-based and refined-food diets are major causes of obesity, diabetes, and other inflammatory disease. Body builders and middle-aged men have adopted it as a way to reduce calories and increase protein for weight loss and muscle building. Women with autoimmune diseases have discovered that versions of the paleo diet can reduce flares and help manage other symptoms. 

What’s on the table?

  • On the table: Meats, poultry, fish/shellfish, fruits, vegetables, nuts and seeds
  • Off the table: Limit food that became available only with farming: legumes, grains, maize, vegetable oils like corn and soy, dairy products, and refined sugar
  • Best for: Psoriasis, MS, see AIP for more specifics
  • Read more about it: diet outline
  • Meal plans & recipes: PaleoGrubs, Paleoleap
  • Meal kits & delivery services: onepaleodelivers, paleohacks 

Now For Some More Specific Diets

The Wahls diet

The Wahls diets was designed by Dr. Terry Wahls, who was diagnosed with multiple sclerosis (MS). The tale is a classic road to recovery through dieting that many of us are familiar with. It is broadly based on the paleo diet, with some modifications.

Looking to diets as a means of mediating autoimmune symptoms
Source: Dr.kellyann
  • On the table: Lots of fish, meat, and vegetables. Focus on leafy greens and brightly colored fruits (high in antioxidants). Obtain fat from animal and plant sources (emphasis on omega-3 fatty acids).
  • Off the table: Avoid dairy products, eggs, legumes, nightshade vegetables, (e.g., tomatoes, eggplant, potatoes, and peppers), grains and sugar
  • Best for: Designed and followed by a doctor with MS, recommended for MS patients
  • Read more about it: diet outline
  • Meal plans & recipes: terrywahls.com

Autoimmune Protocol

The autoimmune protocol is another variation on the Paleo diet, designed specifically for autoimmune patients. The most recent of the autoimmune-specific diets, this one follows a basic paleo diet with the addition of a 30-day elimination and reintroduction diet for certain foods. It was originally developed by Dr. Loren Cordain, who discovered that certain foods allowed on the paleo diet could trigger inflammation in people with autoimmune diseases.

Screen Shot 2018-07-27 at 4.02.01 PM
Source: The Paleo Mom

Both Dr. Robb Wolf and Dr. Sarah Ballantyne (The Paleo Mom) have written articles and books on AIP. This diet focuses on consuming nutrient-rich foods in addition to eliminating likely problematic foods.

  • On the table: Non-starchy vegetables, some starchy vegetables (plantains, parsnips, squashes, sweet potatoes), grass-fed meats, poultry, seafood, herbs, non-seed spices, honey, maple syrup (in limitation), fruit, coconut, fermented products (including dairy, beverages and vegetables), olive and coconut oil, and non-grain flours.
  • Off the table: Grains, beans, legumes (including green beans), nightshade vegetables, refined sugars, eggs, nuts, seeds (including chocolate, coffee and seed-based spices), vegetable oils, and most dairy.
  • Best for: IBS, IBD, recommended for any inflammatory disease
  • Read more about it: diet outline, The Paleo Mom, phoenixhelix
  • Meal plans & recipes: meatified, Paleo Mom Recipes, unboundwellness
  • Meal kits & delivery services: Paleoonthego


FODMAPs is short for Fermentable Oligo-, Di-, Mono- saccharides, And Polyols. These short-chain carbohydrates are poorly digested and absorbed in the small intestine. This makes them a big source of food for microbes in the large intestine. As your microbiome digests the FODMAPS, they can trigger a multitude of GI-related symptoms such as gas, bloating, diarrhea and cramping. Different people may be sensitive to different ones, so in order to personally figure out which ones are triggers for you, this diet starts as an elimination diet–cutting all possible trigger FODMAPs–followed by a reintroduction phase.

FODMAPs considers how the food we eat impacts the microbes in our intestines.
Source: Schar

The first extremely restrictive phase is meant to be temporary, allowing your immune system and microbiome to reset, while the reintroduction phase helps you pinpoint which specific FODMAPs are triggers for you. Once the reintroduction phase is complete, you should have a better understanding of which FODMAPs to avoid, and which ones are OK for you.

  • On the table: (low FODMAP foods) brown rice, buckwheat, oats, maize, arugula, kale, spinach, green beans, carrots, eggplant, tomato, zucchini, low-fructose fruits (blueberries, kiwi, oranges, strawberries), tofu, eggs, seeds, nuts, maple syrup, low-lactose dairy (dry and aged cheeses, cream, yoghurt, etc. (click here for a more complete list)
  • Off the table: (high FODMAP foods): wheat, onions, garlic, high-fructose fruits (apples, apricots, bananas, cherries), asparagus, Brussels sprouts, cauliflower, baked beans, agave nectar, high-lactose dairy (cottage and cream cheese, etc.) (click here for a more complete list)
  • Best for: IBS, recommended for IBD, eczema, MS, fibromyalgia, and rheumatoid arthritis
  • Read more about it: diet outline
  • Meal plans & recipes: dietingwell, alittlebityummy, grocerylist

The Specific Carbohydrate Diet

This diet is an older carb-limiting diet, initially created by Sidney Haas in 1951, and made popular by the book Breaking the Vicious Cycle: Intestinal Health Through Diet written by Elaine Gottschall. SCD has been clinically shown to help people with IBD (6). Unlike Atkins or other low-carb diets, it focuses not on reducing the intake of all carbohydrates, but just on eliminating disaccharides and most polysaccharides, in favor of monosaccharides. Homemade yogurt fermented for at least 24 hours is a major component of this diet, in order to introduce probiotics to correct the dysbiosis experienced by IBD patients.

  • On the table: Non-starchy vegetables, squashes, nightshades, most fruits, meats, poultry, seafood, nuts, seeds, nut-flour, dry-curd cottage cheese, eggs, spices, herbs, as well as fermented yogurt and vegetables.
  • Off the table: Starchy vegetables (potatoes, parsnips, sweet potatoes), lactose, soy, corn, grains, beans, legumes, sugar, chocolate and most food additives and preservatives.  
  • Best for: IBD, Crohn’s, Ulcerative Colitis, Celiac and IBS
  • Read more about it: diet outline
  • Meal plans & recipes: nomorecrohns, elanaspantry
  • Meal kits & delivery services: mypaleos.com

The GAPS (Gut And Psychology Syndrome) Diet,

GAPS was developed by Dr. Natasha Campbell-McBride in the hope of a creating a nutritional lifestyle protocol for healing (7). In her book, she explains how autoimmunity develops and discusses the psychology around the diet and how it works. The diet is designed as a three-part progression diet, starting with an introductory phase, to the full GAPS diet, followed by a small reintroduction phase.

  • On the table: Non-starchy vegetables, squashes, nightshades, meats, poultry, seafood, eggs, nuts, seeds, spices, herbs, honey, fruit, dry aged (30+ days) cheeses, fermented products (vegetables, beverages, dairy) and chocolate.
  • Off the table: Starchy vegetables (potatoes, parsnips, sweet potatoes), grains, beans, legumes, sugars (maple syrup and coconut sugar included), okra, seaweed, most dairy, and starchy-non grain flours.
  • Best for: Autism, ADHD, IBD, recommended for any inflammatory/autoimmune disease
  • Read more about it: diet outline
  • Meal plans & recipes: purposefulnutrition, deliciouslyorganic, draxe.com
  • Meal kits & delivery services: mypaleos.com

Try different diets to find the one best for you!

Screen Shot 2018-07-27 at 4.13.56 PM
Source: Jualmobil

You may have tried one or several of these diets, or maybe none at all. Wherever you are in your nutritional health journey, use this diet break down to help shorten your path. We encourage you to explore and experiment with your options. Learn about many, experiment, compare, contrast and combine diets to figure out what works for you. Get creative! Listen to and trust your gut! Any, all, or none of these may or may not be right for you. Feel free to blend different ideas that resonate with your body. Include your knowledge about your genetics, family history, and your own experiences with different foods and supplement products, to craft your own immune-specific diet that works for you and your symptoms.

Written by: Bonnie Feldman, DDS, MBA, Becca Malizia, BS, Ellen M. Martin


  1. Learn more about your dietary tools, techniques and testing companies here
  2. Discover your uniqueness in our first Food Matters post here
  3. Read about pre- and probiotics, antibiotics and food here
  4. look at some food hacks you can do right now here


  1. “What is Gluten?” Celiac Disease Foundation.   https://celiac.org/live-gluten-free/glutenfreediet/what-is-gluten/ . Accessed 4 August 2018.
  2. “A Brief History of the Gluten-Free Diet: Where Do We Stand?” CeliAct. https://celiact.com/blogs/the-celiact-blog/a-brief-history-of-the-gluten-free-diet-where-do-we-stand . Accessed 4 August 2018.
  3. “The Origins of Celiac Disease: Willem-Karel Dicke: Pioneer in Gluten-free Diet in the Treatment of Celiac Disease.” https://www.celiac.com/articles.html/the-origins-of-celiac-disease/willem-karel-dicke-pioneer-in-gluten-free-diet-in-the-treatment-of-celiac-disease-r1601/ . Accessed 4 August 2018.
  4. “The Development of Agriculture.” National Geographic. https://genographic.nationalgeographic.com/development-of-agriculture/ . Accessed 4 August 2018.
  5. “Hunter Gatherers.” History. https://www.history.com/topics/hunter-gatherers . Accessed 4 August 2018.
  6. Kakodkar, Samir et al. “The Specific Carbohydrate Diet for Inflammatory Bowel Disease: A Case Series.” Journal of the Academy of Nutrition and Dietetics. Vol 115. 1226-1232. 2015. https://www.sciencedirect.com/science/article/pii/S2212267215005043 . Accessed 4 August 2018.
  7. “Autoimmune Diets: SCD vs. GAPS vs. AIP.” Empowered Sustenance. 2012. https://empoweredsustenance.com/scd-vs-gaps-which-is-right-for-you/ Accessed 4 August 2018.


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