Causes and Risk Factors of Food Intolerance

Food intolerance, also referred to as food sensitivity, occurs when a person has difficulty digesting a certain food. It is commonly caused by a lack of digestive enzymes, a sensitivity to food chemicals, or toxins that have contaminated the food.

"Food intolerance" is sometimes confused with "food allergy." However, the two terms should not be used interchangeably. A food intolerance mainly concerns digestion and is usually not life-threatening. In contrast, a food allergy involves the immune system and has the potential to lead to a serious and even life-threatening reaction.

This article will discuss common causes and risk factors associated with food intolerance.

Woman with lactose intolerance

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Common Causes

Food intolerance usually is experienced in the digestive tract. Problems digesting certain foods is thought to be caused by genetics, lack of digestive enzymes, digestive disorders, or sensitivity to food additives. It can also be caused by toxins in the foods we eat.


While research has linked genetics with food allergies, less is known about its relation to food intolerance. However, some metabolic food disorders such as lactose intolerance can be inherited. Lactose intolerance is considered an inherited deficiency of the enzyme lactase.

People with Asian, African, and Native American heritage are more prone to lactose intolerance than other populations.

Lack of Digestive Enzymes and Enzyme Defects

Digestive enzymes are secreted by the gastrointestinal (GI) system. They help with digestion by breaking down fats, proteins, and carbohydrates. Digestive enzymes also aid in nutrient absorption.

Some food intolerance stems from a lack of digestive enzymes. For example, a person with lactose intolerance often lacks enough of the digestive enzyme lactase. Lactase breaks down lactose commonly found in dairy products such as milk.

Fructose intolerance, also known as hereditary fructose intolerance, is another condition caused by a lack of digestive enzymes. It is thought to be caused by mutations in the ALDOB gene, which aids in making the aldolase B enzyme found in the liver. Aldolase B is responsible for breaking down fructose to allow it to be used by the body for energy.

Non-Celiac Gluten Sensitivity

The exact cause of non-celiac gluten sensitivity remains unknown. However, researchers define it as a nonallergic, non-autoimmune condition characterized by gastrointestinal symptoms caused by consuming gluten-containing grains.

Gluten intolerance is often confused with Celiac disease, but they are not the same. A person with gluten intolerance experiences gassiness, bloating, or diarrhea after consuming foods like wheat, barley, or rye. In contrast, Celiac disease is an inherited autoimmune condition that causes damage to the small intestine.

Intolerance to Chemicals in Foods and Additives

There are many chemicals in the foods we eat. Although many people do not have difficulty digesting chemicals found in food, some people do.

While the cause is not completely understood, the following food chemicals are believed to cause unwanted gastrointestinal symptoms in some people:

  • Salicylates are compounds found in plant foods such as green apples, carrots, cucumbers, and herbs. They are thought to overstimulate leukotriene production, which may lead to increased inflammation and smooth muscle contraction.
  • Amines (histamines) can be found in ripe cheese, cured and processed meat, and wine. People who cannot effectively process a large amount of histamine at a time may exhibit gastrointestinal symptoms after consuming foods that are high in amines.
  • Monosodium glutamates (MSG) is a common flavor enhancer in many foods. It's commonly found in Chinese food, processed foods, and meats. It's also found naturally in cheese and tomatoes. The exact cause of this intolerance remains unknown. However, studies have shown that removing MSG from the diets of patients with irritable bowel syndrome (IBS, a common disorder affecting the large intestine) resolves over 30% of symptoms in 84% of patients.
  • Caffeine increases adrenaline production, which gives you energy. It also suppresses a chemical called adenosine, which helps you sleep. When your body does not digest caffeine properly, it can magnify the effect on your endocrine system, leading to restlessness, bloating, and abdominal pain.

Toxins and Food Poisoning

Some foods have natural toxins or chemicals that can cause toxic effects and lead to symptoms similar to a food intolerance.

Toxins and bacteria in foods like mushrooms, potatoes, and spoiled fish are among the most common toxic food intolerances.

Gastrointestinal Disease

Food intolerance appears to be more common in those with underlying digestive disorders. According to one study, patients with IBS, 84% reported symptoms of intolerance to at least one food product. The most common food intolerance reported was to dairy products, beans, lentils, and histamine-releasing foods such as milk, wine, and beer.

Additionally, people with inflammatory bowel disease (IBD) are likely to also have a food intolerance. In a survey given to patients with IBD, an estimated 66% with Crohn's disease (inflammation found anywhere in the wall of the digestive tract) and 64% of patients with ulcerative colitis (inflammation of the lining of the large intestine) reported food intolerance. Common foods causing intolerance in these groups include chocolate, artificial sweeteners, fats, and dairy.

Lifestyle Risk Factors

At some time, you may be unable to tolerate foods you once enjoyed. Some studies reveal women over the age of 60 are more likely to experience a food intolerance over other groups. Moreover, geographical location also tends to play a role in developing a food intolerance.

Research also shows the late introduction of solids in an infant's diet may also cause a food intolerance or allergy to develop later in life.

Additionally, those who have a history of weight loss surgery, such as Roux-en-Y gastric bypass surgery, may experience difficulty tolerating certain foods.

Common Trigger Foods

Trigger foods commonly associated with food intolerance include:

  • Cheese
  • Eggs
  • Nuts
  • Fish
  • Shellfish
  • Onions
  • Garlic
  • Citrus fruits
  • Fried foods


There are several causes of food intolerances, including enzyme deficiencies, problems processing certain chemicals, and sensitivities to certain additives in foods. Having underlying gastrointestinal diseases is also associated with food intolerances.

If you have a reaction to a certain food after eating it, have a discussion with your healthcare provider to determine what is causing your symptoms.

A Word From Verywell

Food intolerance can be challenging to diagnose. Knowing the causes and risk factors can help you better understand why you may be experiencing difficulty digesting certain foods.

Because symptoms of food allergies and food intolerance often overlap, it's important to speak with your healthcare provider to discuss your symptoms and get a diagnosis. Healthcare providers who specialize in food allergies and food intolerance can help you develop a treatment plan to minimize unpleasant reactions.

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Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
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By Lindsey DeSoto, RD, LD
Lindsey Desoto is a registered dietitian with experience working with clients to improve their diet for health-related reasons. She enjoys staying up to date on the latest research and translating nutrition science into practical eating advice to help others live healthier lives.