What Causes Food Intolerances?

Nobody really knows for sure what causes food intolerances.

Research is beginning to help us uncover some of the likely reasons, but here at Healthpath we believe that food intolerances are at least partly caused by poor gut health.

That’s because we see a lot of people being able to tolerate more foods when they pay attention to their gut health with the right diet, lifestyle and supplements.

Read on to find out about food intolerances and what you can do about them.

What is food intolerance?

Food intolerances aren’t allergies. People often mix the two up, but true allergies set off a very strong immune reaction, whereas food intolerances only provoke a small immune reaction, or perhaps none at all (experts disagree about this).

If you’re not sure if you have a food intolerance or an allergy, there are a number of tests you can take that analyse the immune chemicals your body releases when you eat a certain food. Our food intolerance tests measure your IgG levels. IgG stands for immunoglobulin G: a type of antibody which your body can form when you react to foods) levels.

Like almost all tests, food intolerance tests aren’t 100 percent accurate. They’re not suitable to use as a ‘black and white’ template to base your food choices on for the rest of your life, because eating the most diverse diet possible is extremely important for every aspect of your health.

However, food intolerance tests can be very useful as a guide: a good starting place to experiment with taking certain foods out of your diet and watching your symptoms.

At Healthpath, we use a simple at-home finger prick blood test to measure food-specific IgG antibodies to identify the foods you could be intolerant (not allergic) to.

If you have allergies, a different type of antibody called IgE (immunoglobulin E) is likely to be high. If you suspect you have allergies, always tell your GP.

Food intolerances happen when your body reacts to food because it’s unable to digest or break it down. This can happen for endless reasons. For instance, your body may lack the enzyme to break down a particular part of that food. This is the case with the lactose in dairy, if you have a lactose intolerance.

You may also be sensitive to certain chemicals naturally present in food (more on that later)!

If you have a food intolerance, your reaction can happen anything from a few hours to a few days after you eat the food you’re sensitive to. How much of it you eat and which other foods you eat in the same meal can also make a difference to your reaction. 

According to the NHS,1 a food allergy:

  • is a reaction by your immune system (your body’s defence against infection). Your immune system mistakenly treats proteins found in food as a threat
  • can trigger allergy symptoms, such as a rash, wheezing and itching, after eating just a small amount of the food (these symptoms usually happen quickly)
  • is often to particular foods. Common food allergies in adults include fish and shellfish and nut allergies. Common food allergies in children include milk, eggs, fish, peanuts and other nuts 
  • can be life-threatening

While a food intolerance:

  • does not involve your immune system. There is no allergic reaction, and it is never life-threatening
  • causes symptoms that happen gradually, often a few hours after eating the problem food
  • only results in symptoms if you eat a substantial amount of the food (unlike an allergy, where just traces can trigger a reaction)
  • can be caused by many different foods
  • Food intolerances develop because of problems with the functioning of the digestive system, such as leaky gut.

It’s worth noting here that some research has revealed that intolerances do involve the immune system, just in a different way to allergies.2

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Sudden food intolerance in adults

If you’ve developed a sudden food intolerance as an adult, you’re not alone.

Research has now proven beyond doubt that your microbiome (the bacteria and other microorganisms that live in your gut) has a huge bearing on your health.³

Recent findings tell us that the microbiome plays a key role in the development of both allergies and intolerances.⁴ 

We don’t have any data on this, but we know from speaking to thousands of customers that people often report sudden food intolerances after taking medication like antibiotics, or after a stressful period in their life. Pregnancy appears to bring about food intolerances for some women, while it can reverse food intolerances for others!

Why do food intolerances develop?

Nobody knows for sure why food intolerances (or allergies) develop. Experts have some ideas, but it’s important to say that at this stage, we don’t have a lot of research to back these claims up.

For instance:

Gut dysbiosis (an imbalance of the communities of bacteria and other microbes in your gut)

Dysbiosis compromises your gut immunity and digestive power, and increases your chances of leaky gut (which has in fact been linked in research to food intolerances and allergies).⁵

Hygiene hypothesis

Sterile, germ-free environments don’t allow your immune system to develop properly. It then ‘overreacts’ when it comes across allergens. Allergies are much less common in rural environments.6  

Improper weaning

Some experts say that children should be exposed to allergens like wheat earlier, while others say that delaying exposure can decrease the incidence of allergies. Breastfeeding has been proven to reduce allergies.7 

Chemical exposure

The use of pesticides and food additives could mean that your body gets ‘confused’ between the chemicals and the foods they’re used with.

Processing of food

Many people suggest that our bodies cannot recognise the altered proteins in genetically modified or processed food.


We only started eating wheat and dairy ten thousand years ago: a tiny fraction of our evolutionary history. It could be that eating too much of them leads to food intolerances and/or allergies.

Poor nutrition

Our nutrient-poor, calorie-dense diets compromise our immune systems. Poor diets are the leading cause of immunodeficiency worldwide.8

Specific causes of food intolerances

As we explained before, we don’t know exactly what causes food intolerances. However, we do know which foods—or components of foods, to be more precise—are most likely to give you your symptoms.

Here are some of the most common offenders:


Commonly found in:

Any dairy product. For example:

  • Milk
  • Cheese
  • Ice cream
  • Yogurt

What it is:

A carbohydrate, or sugar, found in all milk products to a greater or lesser extent.

Why it causes food intolerance

Lactose is a ‘disaccharide’. That means a type of sugar made up of two molecules. To digest lactose, your body needs to produce an enzyme known as ‘lactase’, which splits the two molecules apart. 

Not all of us have the gene that enables us to produce lactase after we’re babies (all human babies produce it). In fact, only 13 percent of ethnic Chinese adults9 produce lactase. Gut dysbiosis and some diseases can also hamper our ability to produce lactase.


Commonly found in:

  • Fruits
  • Vegetables
  • Honey

What it is:

Fructose is another type of carbohydrate, or sugar: a monosaccharide, to be precise. 

Why it causes food intolerance

There are a few different types of fructose intolerance. The most common is fructose malabsorption. It affects 40 percent of people in the western hemisphere.

We don’t know exactly why some people suffer from it and others don’t, but we suspect it’s a combination of genetics, lifestyle factors (like gut health), exposure to fructose, and overall health.

People with fructose malabsorption cannot properly absorb or digest fructose. As a result, fructose passes into the large intestine, causing gas, diarrhoea and pain.


Commonly found in:

  • Wheat 
  • Barley
  • Rye
  • Triticale
  • Spelt
  • Kamut
  • Couscous

What it is:

Gluten is a general name for the proteins found in wheat. Gluten helps foods maintain their shape, acting as a glue that holds food together. 

Why it causes food intolerance

Gluten intolerance is still controversial, with many doctors claiming that coeliac disease (a gluten allergy) is the only reason you shouldn’t eat gluten.

However recent research is proving otherwise. Alessio Fasano, a Harvard gastroenterologist, found that in gluten sensitivity, your immune system can respond to gluten by fighting it directly. That creates inflammation both inside and outside the digestive system, with documented effects on the brain,10 thyroid function11 and more.

Coeliac disease is different. It’s an autoimmune disease, which involves miscommunications between immune system cells that lead them to fight your body’s own tissues, creating the damage to the intestinal lining seen in coeliac disease.


Commonly found in:


Raisins, prunes, apricots, blackberries, blueberries, cherries, cranberries, grapes, pineapples, plums, oranges, tangerines, strawberries, guava


Broccoli, cucumbers, okra, chicory, endive, radish, zucchini, watercress, alfalfa sprouts, eggplant, squash, sweet potato, spinach, artichokes, broad beans


Curry, aniseed, cayenne, dill, ginger, allspice, cinnamon, clove, mustard, cumin, oregano, pimiento, tarragon, turmeric, paprika, thyme, rosemary

Other sources

Tea, rum, wine, cordials, vinegar, gravies, mints, almonds, water chestnuts, honey, licorice, jam, chewing gum, pickles, olives, food colourings, aloe vera

What it is:

A salicylate allergy or intolerance is a reaction that happens when you come in contact with salicylates, (also known as salicylic acid). Salicylates are found in almost all plants. 

Why it causes food intolerance

One theory is that salicylate sensitivities are caused by an overproduction of leukotrienes, (chemicals involved in your body’s inflammation process) which have been linked to a variety of conditions, including asthma, rheumatoid arthritis and inflammatory bowel disease.12

The buildup of leukotrienes in the body leads to symptoms related to salicylate intolerance.

The most common symptoms involve the respiratory tract. However, the skin and intestinal tract may also be affected.

Symptoms can include:13 

  • Stuffy nose
  • Sinus infection and inflammation
  • Nasal and sinus polyps
  • Asthma
  • Diarrhoea
  • Gas
  • Abdominal pain
  • Gut inflammation (colitis)
  • Hives
  • Tissue swelling

Food poisoning

Commonly found in:

You can get food poisoning from any food or drink contaminated with infectious organisms (usually bacteria). However you can also get food poisoning from viruses and parasites, or their toxins.

What it is:

Food poisoning symptoms vary. Most types of food poisoning cause one or more of the following signs and symptoms:

  • Nausea
  • Vomiting
  • Watery or bloody diarrhoea
  • Abdominal pain and cramps
  • Fever

These symptoms are all part of your body’s way of expelling the infection from your body. They may not be pleasant, but they’re necessary!

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Why it causes food intolerance

A lot of people report food intolerances after a bout of food poisoning.

A 2021 study in the journal Nature found that food poisoning changed many people’s reactions to food that they were able to eat before the infection.14

Many people with IBS remember their symptoms beginning after an upset stomach or vomiting bug. 

This particular study showed a particular type of immune reaction (IgE) to be responsible for symptoms of stomach pain and other IBS symptoms.

Food additives 

Commonly found in:

Food additives are in almost all processed foods. A good way to avoid them is to only eat whole, unprocessed foods! They usually fall into one or more of the following categories:

  • Antioxidants
  • Artificial colourings
  • Artificial flavourings
  • Emulsifiers
  • Flavour enhancers
  • Preservatives
  • Sweeteners

Specific types of additives that you may react to include:


These preservatives are common in processed meats. Symptoms of an intolerance can include headaches and hives.

Monosodium glutamate (MSG)

This is a common flavour enhancer you’ll find in a lot of crisps, savoury snacks and salty foods. It can give you headaches, chest tightness, nausea, and diarrhoea.


Wine, dried fruits, and shrimps are all sources of sulfites. If you have an intolerance, you might experience chest tightness, hives, diarrhoea or even anaphylaxis.

What it is:

The food industry claims that all additives are safe, but many experts believe that a number of them can cause problems for some people. 

Why it causes food intolerance

There are thousands of different food additives. While it’s impossible to state precisely why any one of them might give you uncomfortable symptoms, researchers have begun to look into how ‘safe’ some of them might be.

For instance, one study15 showed that food additives used to thicken and stabilise processed foods may disrupt the bacterial makeup of the gut, causing health problems.

In the study, mice that were fed two chemicals commonly added to foods gained weight, had altered blood sugar and developed intestinal problems. These particular chemicals were emulsifying agents, very common additives that hold together food products that include fat and water, which would otherwise separate.

One of the study’s co-authors, Benoit Chassaing, a microbiologist at Georgia State University in Atlanta, told science news website Live Science: “We are just bombarded with these things [additives].

“People who want to avoid these food additives should eat more whole foods and fresh foods. Packaged products are very loaded with emulsifiers and freshly cooked foods are not, so this is one of the simplest ways to avoid these agents.”

How to work out what is causing your food intolerance

Food allergies, sensitivities and intolerances can go unnoticed for years.

You might have no idea that the foods you eat every day are causing your symptoms.

Unfortunately, the only way to work out which ones could be bothering you is to systematically remove the most common offenders from your diet.

At Healthpath we use a wide range of elimination diets with our customers. Our practitioners choose the best one for each customer based on their health history, their symptoms and their food diary. After following the diet for a number of weeks, we recommend that you reintroduce foods one by one and watch what happens to your body.

Many people find that they can reintroduce foods after a few months of cutting them out. All our elimination diets are nutrient-dense, whole-food eating plans that aim to heal your gut lining and promote a healthy microbiome. By improving your overall gut health, intestinal permeability and digestion, you might find that you enjoy your favourite foods—in moderation—again. 

Key takeaways

  • Food intolerances and food allergies are very different. Food allergies involve a measurable ‘IgE’ immune reaction, whereas food intolerances may involve a different kind of immune reaction.
  • Many experts believe that food intolerances are at least partly caused by poor gut health and changes in your microbiome, brought on by illness, medications or pregnancy, for example.
  • You can be intolerant to almost any food, but some of the most common food intolerances include gluten, milk, salicylates (in fruits and vegetables) and food additives
  • The only reliable way to identify food intolerances is by going on an elimination diet that removes the foods most likely to be bothering you, before reintroducing them one by one.
  • You should always do any kind of elimination diet under the guidance of a Functional Medicine Practitioner or Registered Nutritional Therapist, who will aim to diversify your microbiome and heal your gut lining at the same time, giving you the best chance of success.


Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.

Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.


  1. https://www.nhs.uk/conditions/food-intolerance/
  2. https://pubmed.ncbi.nlm.nih.gov/26030116/
  3. https://pubmed.ncbi.nlm.nih.gov/31315227/
  4. https://www.nature.com/articles/s41575-018-0064-z
  5. https://pubmed.ncbi.nlm.nih.gov/21070397/
  6. https://pubmed.ncbi.nlm.nih.gov/25620193/
  7. https://pubmed.ncbi.nlm.nih.gov/22189253/
  8. https://pubmed.ncbi.nlm.nih.gov/9250133/
  9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6308090
  10. https://pubmed.ncbi.nlm.nih.gov/30340384/
  11. https://pubmed.ncbi.nlm.nih.gov/30060266/
  12. https://pubmed.ncbi.nlm.nih.gov/16835707/
  13. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696737/
  14. https://www.sciencedaily.com/releases/2021/01/210117132238.htm
  15. https://www.nature.com/articles/nature14232

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