A Deep Dive Into Diets: Comparing Autoimmunity Suggested Protocols

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

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 continue to fight this battle with autoimmune disease (or autoinflammatory, or immune-mediated, depending on who you talk to). Although I haven’t found my “optimal diet”, one thing is clear to me, food does matter. Even though I focussed on nutrition during dental school, navigating this new world of autoimmunity, nutrition, and dieting has been complicated and hard. I went gluten free over 10 years ago, and about 3 years ago went dairy-free and reduced my sugar intake. Those three–that is reducing gluten, dairy and sugar–diet modifications seem to be a 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? To answer these questions we did a little digging…

Autoimmune Specific Diets

The gradual rise in autoimmune and other inflammatory diseases over the last century means they now affect some 50 million Americans. But only in the past decade or so, has a focus on nutrition and diet to mediate these symptoms gained great traction.

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Source:  londonclinicofnutrition

Let’s Start With The Most Popular Diets

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

WWII hugely decreased wheat production all over Europe, producing severe shortages of a daily staple. Dutch pediatrician, Dr. Willem-Karel Dicke, found that rates of celiac patients plummeted during the war, and rose again after the war ended, a clue linking celiac disease to gluten (2). In the 1940’s and 50’s, further research found that a diet that eliminated gluten provided complete remission to celiac patients (3). With an increase in awareness, gluten-free has become fundamental in helping people diagnosed with celiac.

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Source: suncoaststandard

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, making this diet one of the easiest to implement.

As most of you know, this diet simply eliminates the protein gluten. This means avoiding all foods containing any wheat, barley or rye ingredients. That can be tough, as gluten naturally occurs in most breads, many cereals, and is often added to processed foods. Luckily, there are many non-gluten grains and starch substitutes that you can eat, such as 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 overly promoted and overpriced specialty foods and the practice of labeling obviously non-grain origin foods (meat, vegetables, soda, water) as gluten free.

  • 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, based on following a diet more like that of  our pre-agricultural ancestors, people who lived during the Paleolithic (Stone Age or caveman) time period. 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, even millions of years, our hominin ancestors hunted meat and gathered nuts and fruits rather than planted and harvested grains and legumes, eating very differently than we do today (4,5). Therefore, presumably our genes have not caught up with the dietary change yet, so that food sensitivities to agricultural products are more common in the population. Some Paleo dieters also avoid dairy, on the grounds that while animal domestication continued older practices 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.

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Source: thewashingtonpost

Motivations for paleo dieters vary. Some are avoiding grain proteins (like gluten) that are suspected of triggering sensitivity reactions. Others believe that grain-based and especially refined-food diets are major causes of the epidemic 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. 

  • 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 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.

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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 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.

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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

Low FODMAP (Fermentable Oligo-, Di-, Mono- saccharides, And Polyols). These short-chain carbohydrates are poorly digested and absorbed in the small intestine, thus are 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.

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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 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, 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.

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Source: mybariatriclife
  • 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

Back To You

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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.


  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.


  1. This is a great breakdown of the myriad autoimmune diets, all with their strengths! I hope you do piece together your own “optimal diet” and stress reduction/exercise/lifestyle combination that works for you (and medical treatments if that ends up being what it takes for you)!

  2. I heard about this AIP! I personally do not have it but I became really curious about this autoimmunity disease! I found this blog really interesting to read! Continue doing a great job!

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