Diagnosing food intolerance

March 22, 2017


Diagnosing food intolerance

Natural Standard Monograph, Copyright © 2013 (www.naturalstandard.com). Commercial distribution prohibited. This monograph is intended for informational purposes only, and should not be interpreted as specific medical advice. You should consult with a qualified healthcare provider before making decisions about therapies and/or health conditions.

Related Terms

  • Additives, allergies, allergy, celiac disease, coeliac disease, celiac sprue, elimination diet, gluten, gluten-free diet, IBS, irritable bowel disease, food additives, food allergies, food allergy, food diary, food intolerance, food intolerance diagnosis, hydrogen breath test, lactose intolerance, sensitivity to food additives.


  • Food intolerance is a non-allergic adverse reaction to food. It can occur for a number of reasons. For instance, the digestive system may become irritated or be unable to break down certain food components. In other cases, toxins may be present in foods, or there may be structural abnormalities in the body.

  • The most common food intolerances include lactose intolerance (inability to digest milk sugar), celiac disease (gluten intolerance), and sensitivity to food additives.

  • Common symptoms of food intolerances include: stomach pain, gas, cramping or bloating, diarrhea, constipation, nausea, vomiting, headaches, and irritability or nervousness.

  • Although the term "food intolerance" is often used interchangeably with "food allergy," they are not the same. A food allergy involves the immune system. This type of reaction occurs when the immune cells overreact to harmless food proteins. During the allergic reaction, the body releases chemicals that trigger symptoms that can than affect the eyes, nose, and throat, as well as the skin and the lungs. Even a trace amount of the allergen can cause a reaction in sensitive individuals. Symptoms of a food allergy may include hives, shortness of breath, swelling of the airways, itchiness, and/or anaphylaxis.

  • Food intolerances are generally diagnosed through trial and error to determine which foods may be causing the intolerance symptoms. By taking an extensive medical history, potential triggers of the intolerance may be determined. Multiple diagnostic procedures can then be performed to determine the exact cause of the intolerance.


  • General: Food intolerance is a non-allergic adverse reaction to food. It can occur for a number of reasons, including the irritation of the digestive system, the inability to break down certain food components, the presence of toxins in foods, or structural abnormalities in the body.

  • Food diary: The first step in diagnosing food intolerance is pinpointing the cause of the symptoms. Patients may be asked to keep food diaries to record foods eaten and when symptoms develop.

  • Elimination diet: Another method to determine trigger foods is the use of the elimination diet. This technique may be used when the food diary indicates multiple trigger foods. The elimination diet involves completely eliminating any suspect foods from the diet until symptoms completely disappear. Once the individual is symptom-free, foods are reintroduced to the diet one at a time to assess symptom recurrence. The elimination diet should only be done under medical supervision to ensure adequate intake of vital nutrients.

  • Once a trigger of the symptoms is determined, the doctor may perform multiple diagnostic tests to further determine the cause of the intolerance (i.e. enzyme deficiency or carbohydrate malabsorption).

  • Hydrogen breath tests: Hydrogen breath tests may be used to diagnose intolerance to lactose, fructose, sucrose, and glucose, as well as intolerances caused by the overgrowth of intestinal bacteria. The breath tests work by exposing the patient to a solution of the suspected intolerance (lactose, fructose, sucrose, glucose) after a period of fasting. The patient then provides breath samples every 60 minutes for three hours, which are then sent to a lab for analysis. The breath samples are analyzed for hydrogen and methane content, which, when elevated, may indicate nutrient malabsorption. These data, along with the information gathered from food diaries and elimination diets, may help to confirm the food intolerance.

  • Stool culture: A stool culture may help determine if a food intolerance is caused by a pathogen (food poisoning) or by an underlying condition. Examination of stool samples may provide information regarding the bacterial composition of the gut and may alert physicians to possible viral or parasitic infections. Additionally, certain conditions, such as gallstones, may alter the composition of the stool (i.e. increased fat content). Testing for digestive or pancreatic enzymes may also be performed on stool samples. This may help confirm enzyme deficiency as a cause of the food intolerance.

  • Serum analysis: Blood testing may be done to rule out a food allergy and other possible causes of digestive symptoms. During the test a sample of blood may be drawn in the physician's office, which is then sent to a lab for analysis.

  • A blood count analysis may be performed to assess infection status.

  • Tests for inflammatory markers, such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR), which may help rule out irritable bowel syndrome (IBS), may also be done.

  • Additional blood tests, such as those for liver and pancreatic enzymes, may also be helpful to determine the cause of digestive symptoms.

  • Physicians may test blood for antibodies, specifically IgE, to rule out a food allergy. The accuracy of IgE testing from blood samples may be limited due to the production of antibodies to other substances. A food allergy can be confirmed through skin testing

  • If celiac disease (an autoimmune sensitivity to wheat gluten) is suspected, blood tests may be performed to determine whether or not the patient has auto-antibodies associated with the disease. Specific auto-antibodies in the blood bind to the patient's own body cells. This triggers other cells to attack and destroy cells in the intestinal lining. If these auto-antibodies are present in a patient's blood, a positive diagnosis is made. Blood tests may also be performed to determine if the patient has antibodies to gluten. During this procedure, a sample of the patient's blood is combined with gluten to determine if antibodies are present. If antibodies are present, it suggests the patient may have celiac disease.

  • Skin test: A skin test may be performed to rule out food allergy. In this test, suspected food substances are placed on the skin of the forearm or back. The skin is then pricked with a small needle to expose the body to a small amount of the potential allergen. If the body initiates an immune response, a small bump or skin reaction, such as reddening, swelling, or a raised, itchy red wheal (bump) that looks similar to a mosquito bite will appear in the area of exposure. If no reactions are seen, the presence of food allergy is ruled out.

  • Imaging: Multiple imaging techniques may be done if IBS, celiac disease, or other conditions are suspected. Endoscopy involves using a lighted tube to visualize, take pictures and biopsy the esophagus, stomach, and small intestines. Sigmoidoscopy and colonoscopy are similar to endoscopy and are used to examine the rectum and colon.


  • General: Food intolerances may be caused by a variety of dysfunctions in the body. By determining the cause of the intolerance and the mechanism behind it, the digestive symptoms may be better managed.

  • Missing enzyme or transport defect: In individuals with a deficiency in enzymes required to digest carbohydrates (i.e. lactase deficiency causing intolerance to milk sugar), or defects in the transporter systems required for their absorption (i.e. GLUT2 or GLUT5 defects in the transport of fructose, glucose and galactose), the carbohydrates that are not broken down and absorbed in the small intestine reach the large intestine in a form the body is not used to. In the large intestine, the carbohydrates are broken down by bacteria into substances that may cause gas, bloating, diarrhea, and abdominal pain.

  • Bacterial overgrowth: Overgrowth of bacteria in the small intestine may produce symptoms similar to those experienced by individuals with enzyme deficiencies. When excessive bacteria are present in the small intestine, carbohydrates are metabolized by the bacteria to produce substances that may cause gas, bloating, diarrhea and abdominal pain. Individuals taking immunosuppressants or proton-pump inhibitors (PPIs) and patients with diabetes mellitus may be at increased risk for bacterial overgrowth.

  • Histamine intolerance: Histamine intolerance may produce symptoms similar to those seen in an allergic reaction. In this case, however, the body is reacting to histamine content in food versus histamine released by the body. Since there is no immune response generated from this reaction it may be considered a "pseudoallergy". Histamine intolerance most often stems from a deficiency of the enzyme diamine oxidase (DAO), which metabolizes histamine in foods. Some histamine-containing foods include aged cheeses, red wine, tuna fish, sausage, and mackerel. Some components in black tea or alcohol may inhibit DAO, also triggering the intolerance. This reaction may produce rash, abdominal pain, flatulence, diarrhea, shortness of breath, runny nose, and heart palpitations.

  • Irritable bowel syndrome (IBS): The exact cause of IBS is unknown, however, it may produce symptoms such as diarrhea, constipation, abdominal pain, flatulence, bloating and increased bowel sounds. It may be caused by a neurotransmitter imbalance. Up to 60% of individuals with the syndrome have psychological symptoms such as anxiety and depression. Research has reported that serotonin (a neurochemical for mood and intestinal movement) is linked with normal gastrointestinal functioning. Serotonin is a specialized type chemical called a neurotransmitter that delivers messages from one part of the body to another. Ninety-five percent of the serotonin in the body is located in the gastrointestinal tract, and the other five percent is found in the brain. Cells that line the inside of the bowel work as transporters and carry the serotonin out of the gastrointestinal tract. People with IBS, however, have fewer places for serotonin to bind, causing abnormal levels of serotonin to exist in the digestive tract. As a result, people with IBS experience problems with bowel movement, motility, and sensation.

  • Food poisoning: Food poisoning is commonly caused by the ingestion of toxins, bacteria, parasites, or chemicals present in spoiled or contaminated water or food. These toxins may irritate the lining of the stomach and intestines causing them to increase production of water and mucous leading to very loose, watery stools and abdominal pain. In severe cases, food poisoning may result in dehydration due to water lost in stool. Some contaminants may cause intestinal bleeding, leading to pain, anemia, and other symptoms, and it may ultimately be fatal.

  • Sensitivity to food additives: Food additives are substances that preserve the flavor or improve the taste of a product. These additives are classified as: dye or coloring agents, antioxidants, emulsifiers or stabilizers, flavoring or taste enhancers, or preservatives. Generally, an intolerance to a food additive or preservative is suspected if a person consistently experiences symptoms of illness after eating certain foods, such as pre-packaged (prepared) foods or those found at a restaurant. While reactions to food additives may include digestive symptoms, respiratory symptoms (such as shortness of breath) and dermatologic symptoms (such as rash) are also common.

  • One of the most common causes of food additive intolerances is sulfites, which are used to preserve dried fruit, canned goods, and wine. Other additives that may cause reactions are the flavor enhancer monosodium glutamate (MSG), colorants, preservatives (such as benzoates, sorbates, and tartrazine), and sweeteners (such as aspartame). The mechanism of the reaction is not fully understood.

  • Psychological factors: It has been suggested that stress or even thinking about a certain food may have the ability to produce digestive symptoms. A clinical study looked at carbohydrate digestion under conditions of stress and relaxation. It was found that under stress conditions, less carbohydrate digestion occurred than under relaxation conditions. This may be due to the production of less amylase (the enzyme responsible for carbohydrate break down) under stressful conditions. Less carbohydrate break down may lead to symptoms similar to those of enzyme deficiencies.

  • Celiac disease: Celiac disease, also called coeliac disease, gluten intolerance, or celiac sprue, is a digestive disorder that occurs when an individual's immune system overreacts to the protein gluten or other proteins within gluten (such as gliadin). Gluten is present in grains, including wheat, rye, barley, and to some degree, oats. When a patient with this disease eats food that contains gluten, the immune system's response damages the intestinal lining. This causes symptoms of abdominal pain and bloating after consuming gluten. Although there is an immune response, celiac disease is considered a food intolerance because the antibodies produced during an allergic reaction are not present.


  • General: Testing for food intolerance should be done under medical supervision. A qualified healthcare provider should be consulted before making decisions about therapies and/or health conditions.

  • Food diaries: Keeping a food diary is generally considered a safe and effective way to pinpoint food intolerances. Keeping a food diary prior to a medical appointment may help diagnosis proceed faster, but maintaining adequate nutrition should remain a priority.

  • Elimination diet: The elimination diet is safe and effective when done under the direction of a medical professional. A qualified healthcare provider can help ensure adequate nutrition while eliminating possible trigger foods.

  • Hydrogen breath test: During hydrogen breath testing the individual ingests fairly large quantities of the possible trigger substance (i.e. lactose). This may induce symptoms similar to what is experienced during the reaction (abdominal pain, bloating, gas, diarrhea, constipation).

  • Stool culture: A stool culture is generally considered safe and painless.

  • Serum analysis: The primary side effects of blood testing are possible discomfort and bruising at the puncture site.

  • Skin test: Skin tests cause minimal, if any, discomfort. The needles used barely penetrate the skin's surface and will not cause bleeding. Some itching may arise if an allergic response does occur.

  • Imaging: Endoscopy, sigmoidoscopy, and colonoscopy are generally considered safe procedures; however, as they are somewhat invasive, they do carry a small risk of bleeding, infection, or tearing of the gastrointestinal tract.

Author Information

  • This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).


Natural Standard developed the above evidence-based information based on a thorough systematic review of the available scientific articles. For comprehensive information about alternative and complementary therapies on the professional level, go to www.naturalstandard.com. Selected references are listed below.

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Copyright © 2013 Natural Standard (www.naturalstandard.com)

The information in this monograph is intended for informational purposes only, and is meant to help users better understand health concerns. Information is based on review of scientific research data, historical practice patterns, and clinical experience. This information should not be interpreted as specific medical advice. Users should consult with a qualified healthcare provider for specific questions regarding therapies, diagnosis and/or health conditions, prior to making therapeutic decisions.


March 22, 2017