Can food intolerance cause stomach problems? Unraveling the link between your diet and gut discomfort

October 13, 2025 •

4 min read

An estimated 15-20% of the population in industrialized nations experience symptoms from food intolerance, which can directly cause uncomfortable stomach problems. Unlike a food allergy, which triggers an immune response, intolerance is a digestive issue that manifests as a physical reaction to certain foods.

Quick Summary

Food intolerance is a digestive issue caused by the body's inability to properly break down certain foods, leading to common gastrointestinal problems like bloating, gas, and abdominal pain. It is distinct from both food allergies and celiac disease, as it does not involve the immune system or cause permanent intestinal damage. Management strategies typically involve dietary modifications under professional supervision.

Key Points

Digestive, Not Immune: Food intolerance primarily affects your digestive system, unlike food allergies which trigger an immune response.
Enzyme Deficiencies: Many intolerances, like lactose intolerance, stem from a lack of specific digestive enzymes needed to break down food components.
Gut Fermentation: When undigested food reaches the large intestine, gut bacteria ferment it, producing gas and causing bloating and discomfort.
Symptoms Vary: Stomach pain, gas, bloating, and diarrhea are common symptoms, but can vary depending on the trigger and amount consumed.
Reliable Diagnosis: The most accurate method for diagnosis is a medically supervised elimination diet, not commercial IgG tests.
Gradual Reintroduction: You may not need to completely eliminate trigger foods; working with a dietitian can help find your tolerance threshold.
Long-Term Strategy: Management is focused on dietary changes to limit or avoid triggers while ensuring adequate nutrition, often with a dietitian's help.

The Digestive Roots of Food Intolerance

When your digestive system struggles to break down certain foods, the resulting unpleasant reaction is known as a food intolerance. This is not an allergic reaction, but rather a mechanical and chemical problem within the gut that often leads to stomach-related symptoms. The root causes can vary, but generally fall into three main categories:

Enzyme Deficiencies

Many food intolerances are the result of a missing or insufficient digestive enzyme. The most classic example is lactose intolerance, where the small intestine doesn't produce enough lactase, the enzyme required to digest the sugar (lactose) found in milk and dairy products. Without enough lactase, the undigested lactose travels to the large intestine, where it is fermented by gut bacteria. This process creates gas, leading to bloating, flatulence, and pain. Other enzyme-related issues can affect the digestion of complex carbohydrates and certain sugars.

Chemical Sensitivity

Some individuals are sensitive to certain naturally occurring food chemicals or additives. Histamine, found in aged cheeses, wine, and processed meats, can cause a range of symptoms, including stomach cramps and diarrhea. Sulfites, often used as preservatives in dried fruits and wines, can also trigger reactions. Similarly, high doses of salicylates, found in fruits, vegetables, and spices, can cause issues in sensitive individuals.

Carbohydrate Malabsorption

Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, or FODMAPs, are short-chain carbohydrates found in a wide variety of healthy foods. In some people, particularly those with Irritable Bowel Syndrome (IBS), these carbs are poorly absorbed in the small intestine. As they pass into the large intestine, they pull in extra water and are fermented by bacteria, causing gas, bloating, pain, and altered bowel habits. This is a very common trigger for people with sensitive guts.

How Intolerance Differs from Allergy and Celiac Disease

It is crucial to understand the differences between a food intolerance, a food allergy, and celiac disease, as their mechanisms and severity vary significantly.


Feature	Food Intolerance	Food Allergy	Celiac Disease
Bodily System	Digestive system	Immune system	Autoimmune disorder affecting the immune system
Mechanism	Lack of an enzyme, sensitivity to food chemicals, or difficulty absorbing nutrients	Immune system mistakenly identifies a protein as harmful, releasing IgE antibodies	Immune response to gluten damages the small intestine lining
Onset of Symptoms	Gradual, hours after eating	Rapid, within minutes to a few hours	Variable, can appear hours or days after consuming gluten
Severity	Uncomfortable but not life-threatening	Can be life-threatening (anaphylaxis)	Can lead to serious, long-term health complications if unmanaged
Quantity Trigger	Dose-dependent; small amounts may be tolerated	Microscopic amounts can trigger a severe reaction	Any amount of gluten can cause damage
Examples	Lactose, FODMAPs, sulfites, histamine	Peanuts, tree nuts, shellfish, milk, eggs	Gluten (from wheat, barley, rye)

Identifying Your Food Triggers

Diagnosis for food intolerance is primarily based on clinical history and dietary changes, rather than a single test.

Start a Food and Symptom Diary: This is a powerful first step. Track everything you eat and drink, noting any digestive symptoms, their severity, and the time they occur. Since intolerance symptoms can be delayed by up to 48 hours, this record can be key to spotting patterns.
Consult a Professional: Work with a GP or registered dietitian who can guide you through the process. They can help rule out other conditions with similar symptoms, like IBS, celiac disease, or inflammatory bowel disease.
Perform an Elimination Diet: Under a professional's supervision, remove suspected trigger foods for 2 to 6 weeks. If your symptoms improve, you can begin the reintroduction phase, adding foods back one by one to pinpoint the exact culprits and determine your personal tolerance level.
Consider Specific Tests: For suspected lactose intolerance, a hydrogen breath test is a reliable option. However, be wary of commercial IgG blood tests, as medical consensus deems them unreliable for diagnosing food intolerances.

Effective Management and Dietary Strategies

Once your triggers are identified, managing food intolerance becomes about finding the right balance for your body. The goal is to minimize symptoms while maintaining a nutritionally complete diet.

Read Labels Carefully: This is essential for avoiding problem ingredients. Look for hidden sources of lactose (like whey), gluten (like malt), and additives (like sulfites). Food companies are required to declare common allergens, but manufacturers’ processes can change, so always double-check.
Don't Restrict Unnecessarily: Many people with intolerances can handle a small amount of the trigger food without symptoms. The elimination diet helps you find your personal threshold. Avoid cutting out entire food groups long-term without professional guidance, as it can lead to nutritional deficiencies.
Use Supplements: For specific intolerances, like lactose, over-the-counter enzyme supplements (lactase drops or pills) can help you digest the food. For other issues, a dietitian might recommend probiotics or prebiotics to support gut health.
Embrace Home Cooking: Preparing your meals at home gives you complete control over ingredients, helping to reduce anxiety about potential triggers. This also allows you to experiment with alternatives and build a library of safe, delicious meals.
Consult a Dietitian: An accredited dietitian with experience in food intolerance is invaluable. They can help create a personalized plan, offer alternative food suggestions, and provide emotional support during a challenging dietary transition. A resource like Food Allergy Canada offers valuable information and expert guidance.

Conclusion: Reclaiming Your Digestive Comfort

Food intolerances can undoubtedly cause significant stomach problems, but they are manageable. By understanding the specific digestive mechanism behind your symptoms and using proven diagnostic methods like a food diary and elimination diet, you can identify your unique triggers. Unlike food allergies or celiac disease, many intolerances are dose-dependent, allowing for flexible management. With professional guidance, careful label reading, and a thoughtful approach to eating, you can regain control of your digestive health and enjoy a varied, nutritious diet once again.

Frequently Asked Questions

A food intolerance involves the digestive system and is typically caused by a difficulty in digesting a certain food component. Symptoms are generally unpleasant but not life-threatening. A food allergy, however, involves the immune system and can cause a severe, life-threatening reaction (anaphylaxis).

Yes, bloating and gas are two of the most common stomach problems caused by food intolerance. This occurs when undigested food ferments in the large intestine, producing excess gas.

Common intolerances include lactose (the sugar in dairy products), gluten (found in wheat, barley, and rye), and FODMAPs (a group of carbohydrates). Some people are also sensitive to food additives or natural chemicals like histamine.

The most reliable method is a medically supervised elimination diet. This involves removing suspected foods for a few weeks and then reintroducing them one by one to monitor your body's reaction. A food diary is also a helpful tool.

Most medical professionals do not recommend commercial IgG food sensitivity tests, as they are not scientifically proven to reliably diagnose food intolerances. They can be misleading and lead to unnecessary dietary restrictions.

Not necessarily. Unlike allergies, many food intolerances are dose-dependent, meaning you may be able to tolerate a small amount of the trigger food without experiencing symptoms. Working with a dietitian can help you find your personal tolerance threshold.

A dietitian provides expert guidance through elimination and reintroduction diets, ensuring nutritional needs are met while identifying triggers. They also teach you how to read labels, suggest alternatives, and create a balanced long-term eating plan.