Autoimmune Diets: SCD vs. GAPS vs. AIP (2024)

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I am a testimony to the power of a nutritional protocol for autoimmunity. At age 14, I received a diagnosed of Ulcerative Colitis, a severe autoimmune disease of the large intestine. I struggled for years with the potent side-effects of ineffective medications. Desperate for a solution, I began a grain free diet and tweaked it as I learned more and more about nutrition. Now, it’s been years since I’ve experienced any symptom of my disease and I’m completely medication-free.

I’ve immersed myself in using all of these nutritional protocols for the last four years. I began with the Specific Carbohydrate Diet. As I learned about traditional foods and nutrient-dense ingredients, I incorporated principles from GAPS. I also tried a 30 day AIP diet to monitor my symptoms with food re-introductions.

Autoimmune Diets: SCD vs. GAPS vs. AIP (1)

In this post, I share with you what I wish I knew at the beginning of my grain free adventure. With the below information, you can tailor a nutritional protocol to your needs.

The Specific Carbohydrate Diet (SCD)

SCD eliminates complex carbohydrates to allow the healing of the intestinal lining. Targeted for Chron’s Disease, Ulcerative Colitis and Irritable Bowel Syndrome, this protocol is clinically shown to support the healing of Irritable Bowel Disease.

Allowed foods

Non-starchy vegetables, squashes, nightshade vegetables, meats, nuts and seeds, eggs, spices and herbs, homemade yogurt, honey, coconut, fruit, cheeses aged 30+ days, dry curd cottage cheese, fermented vegetables.

Foods to avoid

Grains, beans, legumes, sugar (including maple syrup and coconut sugar), mucilaginous vegetables (okra, seaweed), most dairy, starchy vegetables (parsnips, potatoes, sweet potatoes), fermented beverages, chocolate and carob, starchy non-grain flours (tapioca, arrowroot, cassava).

Potentially problematic foods allowed

Eggs, nuts, seeds, nightshades, and dairy products

Points to consider

SCD was developed in the 60’s, when damage to intestinal flora was generally not as severe as it is today. Each generation, exposed to an accumulated load of food and environmental toxins, faces a greater burden on gut flora. SCD may not be intensive enough for many of today’s autoimmune cases.

This diet lacks the focus on nutrient-dense foods found in GAPS and AIP. For example, both GAPS/AIP place strict emphasis on properly sourcing meats and using healthful fats. With an understanding of nutrient-dense foods, however, you can make SCD highly nutritious.

Homemade yogurt, consumed daily, provides the crucial source of gut-balancing probiotics. It is not an optional part of this dietary protocol. The GAPS Diet, on the other hand, emphasizes a variety of fermented foods as well as probiotic supplements to re-balance gut flora.

Key Resources

The Gut and Psychology Syndrome Diet (GAPS)

Developed by Dr. Natasha Campbell-McBride, a clinician with decades of experience in nutritional healing, GAPS is a lifestyle protocol for healing. Targeted at holistic recovery from mental illnesses including autism and ADHD, it is highly successful for autoimmunity of all varieties. It progresses in stages, from a limited Phase 1 to the Full GAPS Diet. After that, individuals may re-introduce other whole foods according to their symptoms. Reintroduction, if tolerated, includes dried legumes and properly soaked grains.

Allowed foods

Non-starchy vegetables, squashes, nightshade vegetables, meats, eggs, nuts and seeds, spices and herbs, honey, coconut, fruit, cheeses aged 30+ days, dry curd cottage cheese, fermented vegetables, fermented dairy products, fermented beverages, carob/chocolate.

Foods to avoid

Grains, beans, legumes, sugar (including maple syrup and coconut sugar), mucilaginous vegetables (okra, seaweed), most dairy, starchy vegetables (parsnips, potatoes, sweet potatoes) starchy non-grain flours (tapioca, arrowroot, cassava).

Potentially problematic foods allowed

Eggs, nuts, seeds, nightshades, and dairy products

Points to consider

The Introduction Diet often works wonders for those in extreme digestive distress, or those currently suffering a disease flare-up. Depending on symptoms, some individuals choose to start at the full GAPS Diet, rather than phase 1.

I recommend reading The GAPS Book even if you do not follow the protocol. It offers an accessible description of how autoimmunity develops, and explains why the diet works at a physiological level. It also outlines the lifestyle, supplement, and detoxification steps essential for a healing protocol.

GAPS emphasizes nutrient-dense foods including stocks, healthy fats, organ meats and fermented foods. Quality and proper sourcing of these ingredients are also discussed.

Key Resources

The Autoimmune Paleo Protocol (AIP)

The most recently developed protocol, AIP eliminates some of the potential “trigger foods” allowed on GAPS and SCD. It does, however, allow starchy vegetables which may not be well tolerated by those with Irritable Bowel Disease. AIP is a 30 day elimination diet. After the 30 days, a careful reintroduction schedule is implemented. Reintroduction, if tolerated, include eggs, nuts/seeds, nightshades, fresh legumes, and dairy.

Due to increasing popularity, you’ll find many recipes, meal plans, cooking videos, shopping lists and other resources online. AIP emphasizes that the inclusion of nutrient-dense foods is as important as the elimination of problem foods.

Allowed foods

Non-starchy vegetables, squashes, starchy vegetables (plantain, parsnip, sweet potatoes), meats, herbs, non-seed spices, specific sweeteners (honey, maple syrup, coconut sugar), coconut, fruit, fermented vegetables, fermented dairy products, fermented beverages, carob, starchy non-grain flours (tapioca, arrowroot, cassava, tigernut).

Foods to avoid

Grains, beans, legumes (including fresh legumes such as peas and green beans), nightshade vegetables, refined sugar, eggs, nuts and seeds (including chocolate, coffee, and seed-based spices like nutmeg), dairy.

Potentially problematic foods allowed

Starchy vegetables, non-grain flours.

Points to consider

Use moderation and even minimization of the starchy vegetables and starchy flours. Not only can starches challenge a damaged digestive tract, they are concentrated sources of glucose which may spike blood sugar.

In the same way, use the allowed sweeteners such as honey, maple syrup, and coconut sugar judiciously. These concentrated sources of sugar are rare treats, not daily indulgences.

Key Resources

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Autoimmune Diets: SCD vs. GAPS vs. AIP (2024)

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