The exact cause of mouth ulcers is unknown

In some cases they are thought to be caused by an overreaction by the body's own immune system.

Factors that appear to provoke them include stress, fatigue, illness, injury from accidental biting, hormonal changes, menstruation, sudden weight loss, food allergies and deficiencies in vitamin B12, iron and folic acid. Some drugs, such as nicorandil, have been linked with mouth ulcers.

Trauma to the mouth is a common cause of mouth ulcers. Physical trauma, such as toothbrush abrasion, poking with sharp food, accidental biting (this can be particularly common with sharp canine teeth), or dental braces can cause mouth ulcers by breaking the mucous membrane.

Other factors, such as chemical irritants or a burn in the mouth, may also lead to the development of ulcers. However in many cases, the precise cause is unknown.

A common cause of ulcers is gluten intolerance, in which case consumption of wheat, rye, or barley can result in chronic mouth ulcers. If gluten intolerance is the cause, prevention means taking most breads, pastas, cakes, pies, cookies, scones, biscuits, beers etc. out of the diet and substituting gluten-free varieties where available.

Artificial sugars, such as those found in diet cola and sugarless gum, have been reported as causes of mouth ulcers as well. They can also be linked to an increased intake of acids such as ascorbic acid (one form of Vitamin C) or citric acid. In this case the sores disappear after intake decreases (for example, by substituting ascorbate salts for ascorbic acid).

Repeat episodes of mouth ulcers can be indicative of an immunodeficiency, signalling low levels of immunoglobulin in the mucous membrane of the mouth.

Chemotherapy is a common cause of mouth ulcers. Mouth ulcers may also be symptoms or complications of several diseases listed in the following section.

A common urban myth is that mouth ulcers are directly connected to the onset of the herpes simplex virus, but in reality ulcers associated with herpes (or cold sores) are of an entirely different nature from mouth ulcers, which are not contagious.