SCD, GAPS and the autoimmune protocol: what strict elimination diets can and cannot do

Healthy state

Three diets are recommended especially often in gut forums. The Specific Carbohydrate Diet (SCD) allows only simple sugars as in fruit and honey; grains, starch, sugar and most dairy are forbidden. The idea: double and complex sugars are poorly digested and feed harmful bacteria. The GAPS diet ("Gut and Psychology Syndrome") builds on it, starts with broth and fermented foods, and also promises help with autism, ADHD or depression. The autoimmune protocol (AIP) is a stricter paleo diet without grains, pulses, dairy, eggs, nuts, seeds, nightshades, coffee and alcohol, with reintroduction after several weeks.

Some of it is sensible: cooking fresh, little ultra-processed food, plenty of vegetables. And some elimination diets are well studied when they are clearly defined, time-limited and supervised. Low-FODMAP FODMAP Short for fermentable sugars and sugar alcohols that are poorly absorbed in the small intestine, such as fructans, lactose, fructose and sorbitol. More in the chapter “Doing low-FODMAP right” in IBS Irritable bowel syndrome Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis” is one example. For children with Crohn's disease there is the Crohn's Disease Exclusion Diet (CDED) together with formula: in a randomised trial Randomised trial A study in which chance decides who gets the treatment and who does not, for comparison. This makes results particularly reliable. of 78 children, 76 percent were in steroid-free remission after 12 weeks, compared with 45 percent on formula alone followed by a free diet.

There is one large study on SCD. In DINE-CD, 194 adults with mild to moderate Crohn's disease were randomly assigned to SCD or a Mediterranean diet, with prepared meals for the first six weeks. After six weeks, 46.5 percent on SCD and 43.5 percent on the Mediterranean diet were in symptomatic remission, so no difference. Inflammation markers rarely improved in either group. The researchers conclude that the simpler Mediterranean diet is preferable for most people. A small pilot study in ulcerative colitis also found no difference, and more than half dropped out.

For AIP there is a study of 15 people with active inflammatory bowel disease Inflammatory bowel disease Umbrella term for Crohn’s disease and ulcerative colitis: long-term, relapsing inflammation of the gut that needs medical treatment. More in the chapter “Immune system and inflammation”, without a control group. Symptoms and quality of life improved, blood CRP did not. Without a control group it is impossible to separate the effect of the diet from attention, expectation or the natural course. We found not a single controlled study of the GAPS diet.

Disrupted state: causes and effects

The longer the forbidden list and the more open the end, the greater the risks. A 2026 review of self-started elimination diets in inflammatory bowel disease lists malnutrition, micronutrient deficiencies, muscle loss, disturbed microbiota, fear of food and ARFID ARFID Avoidant/restrictive food intake disorder: someone eats too little or too narrowly, not because of body shape or weight, but out of fear of symptoms, low appetite or aversion to tastes and textures. More in the chapter “Fear of food: when your list of safe foods keeps shrinking”. Several professional societies therefore advise against long-term elimination diets and recommend a varied Mediterranean diet.

Fewer plants mean less food for the microbiota. Even the short low-FODMAP phase lowers bifidobacteria. SCD and GAPS also remove grains, starch and partly pulses, the main sources of resistant starch and fibre that butyrate Butyrate A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids” producers live on. How much this changes the microbiota on these diets has hardly been measured in humans.

The reasoning often does not hold. That double sugars and starch are generally poorly digested is not true: enzymes in the small intestine reliably split table sugar and starch in most people. GAPS attributes psychiatric and developmental conditions to the gut and wants to treat them with diet. There is no evidence for this, and it becomes dangerous if effective help is delayed as a result, especially for children.

People who have tried an exclusion diet have features of avoidant/restrictive food intake disorder (ARFID) about three times as often in gut clinics. Whether the diet triggers it or anxious eaters are more likely to diet is open. What is clear: long forbidden lists make it hard to eat relaxed again.

The key difference from low-FODMAP is structure. Low-FODMAP has fixed phases: 2 to 6 weeks of avoidance, reintroduction one by one, then eating as broadly as possible. In a follow-up, relief lasted in 57 percent and the diet remained adequate. SCD and GAPS have no clear end, and reintroduction is either not planned or loosely defined.