Elimination Diet: How to Identify Your Food Intolerances Step by Step

Intolerance, allergy, sensitivity: knowing the difference

Before cutting anything from your plate, an important distinction needs to be made. A food allergy involves the immune system — sometimes with a risk of anaphylaxis — and requires a formal allergological assessment. A food intolerance, on the other hand, is most often non-immunological: it stems from an enzyme deficiency, excessive bacterial fermentation, or osmotic effects in the gut. As for food sensitivity, it remains a diagnosis of exclusion, with no reliable biomarker identified to date.

This distinction matters, because it determines the approach you should take.

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What is an elimination diet?

An elimination diet involves temporarily removing one or more suspect foods, then reintroducing them in a methodical way to observe whether symptoms appear or disappear. It is not a diet in the restrictive sense of the word — it is a structured diagnostic tool.

The indications best supported by the evidence include:

• Coeliac disease (a severe, permanent intolerance to gluten)
• Lactose intolerance
• Irritable bowel syndrome (IBS), particularly through the low-FODMAP protocol

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Understanding the mechanisms: why certain foods cause problems

FODMAPs and fermentation

FODMAPs are fermentable carbohydrates — oligosaccharides, disaccharides, monosaccharides, and polyols — that are poorly absorbed in some people. In the small intestine, they exert an osmotic effect; in the colon, they are rapidly fermented by the gut microbiota, producing gas and intestinal distension. The result: bloating, pain, and disrupted bowel habits. This mechanism is particularly relevant in IBS, which affects between 4 and 11% of the global population.

Lactose

Lactose intolerance is linked to a reduction in lactase activity — the enzyme responsible for breaking down this milk sugar. Approximately 65 to 70% of the world's adult population has some degree of hypolactasia, though not everyone experiences symptoms. The amount tolerated is often individual, and fermented dairy products (yoghurt, aged cheeses) are generally better tolerated.

Gluten or fructans?

In people without coeliac disease, symptoms attributed to "gluten" are often actually caused by wheat fructans — which are, themselves, FODMAPs. Blinded provocation trials suggest that the nocebo effect and other components of wheat also play a role. Gluten is therefore not automatically the culprit outside of coeliac disease or wheat allergy.

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The 3-phase protocol: the method that works

Particularly for IBS, the 2021 recommendations from the American College of Gastroenterology point towards a structured low-FODMAP protocol comprising 3 stages:

1. Short elimination phase (2 to 6 weeks): foods high in FODMAPs are removed — onion, garlic, legumes, certain fruits (apples, pears, mango), milk, and polyols (sorbitol, mannitol).
2. Gradual, tested reintroduction: each food group is reintroduced one at a time, with careful observation of the response.
3. Long-term personalisation: you build a way of eating tailored to your actual tolerance, rather than a generic list of restrictions.

This protocol should ideally be supervised by a trained dietitian, particularly if there is any history of disordered eating or a risk of nutritional deficiency.

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What not to do

Several common mistakes can undermine the process:

• Eliminating gluten without prior testing if coeliac disease is suspected — serological tests and biopsies can return false negatives once gluten has been removed
• Cutting out multiple foods at random, without reintroduction or any form of follow-up
• Relying on unvalidated commercial tests claiming to detect "intolerances" (food-specific IgG tests in particular) — these are not part of current medical recommendations
• Prolonging a restrictive diet indefinitely: diets low in fibre and plant foods can reduce microbiome diversity, with potentially negative consequences for long-term gut health

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Nutrients to watch when restricting your diet

A poorly planned elimination diet can lead to nutritional deficiencies. Pay particular attention to:

• Fibre and prebiotics (essential for the gut microbiome)
• Calcium and vitamin D (if dairy is excluded)
• Iron and folate (if grains or legumes are excluded)
• B vitamins and magnesium

Processed "gluten-free" or "lactose-free" products are not automatically healthier — some contain more refined starches, added sugars, or fats.

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The right approach, in summary

An elimination diet is neither a miracle solution nor a trend to follow. It is a medical tool, effective when it is:

• Targeted at a specific hypothesis
• Temporary and properly supervised
• Followed by methodical reintroduction
• Supported by an appropriate medical assessment

If you are experiencing chronic digestive symptoms, the first step is always to speak with your GP — to rule out any underlying organic conditions before exploring a dietary explanation. Personalisation comes after that. And that is where this kind of approach, properly carried out, can genuinely make a meaningful difference to quality of life.