Poor dental hygiene: If you get recurrent canker sores, your toothpaste may be the culprit. Try a toothpaste that does not contain the detergent sodium lauryl sulfate. This is a detergent that may cause the mucous surfaces in the mouth to dry out, leaving them vulnerable to attack from acidic foods. Do not use the same toothbrush for longer than one month. When canker sores on the gum are healing, it is best to use a very soft toothbrush.

Irritation from dental work: Using a rough, hard-bristled toothbrush, or pressing unduly hard while brushing the teeth. This can irritate the mucous membranes and create a canker sore. 

Food allergies (especially milk and gluten sensitivity): It has been clearly demonstrated that allergic mechanisms are responsible for producing canker sores in many cases. There is considerable evidence that sensitivity to gluten (a protein found in grains) is the primary cause of recurrent canker sores in many cases. The frequency of recurrent canker sores is increased in patients with celiac disease, a condition characterized by diarrhea and malabsorption due to a sensitivity to gluten. Withdrawing gluten from the diet results in complete remission of recurrent canker sores in patients with celiac disease and some improvement in the rest of the patients. 

Non-food allergens: Allergens that commonly induce canker sores include preservatives such as benzoic acid, methylparaben, dichromate, and sorbic acid. Elimination of allergens usually brings complete resolution or significant improvement in people with recurrent canker sores. 

Nutritional deficiencies: Although a number of nutrient deficiencies can lead to canker sores, thiamine deficiency appears to be the most significant.
Deficiencies of iron, lysine, vitamin B12, and folic acid also can lead to canker sores. Several studies showed that nutrient deficiencies are common among recurrent canker sore sufferers than in the general population. A study of 330 patients with recurrent canker sores showed that forty-seven (14.2 percent) were deficient in iron, folate, vitamin B12, or a combination of these nutrients. When these patients' deficiencies were corrected, the majority had complete remission. Other studies have shown similar deficiency rates for the same nutrients and equally good response to supplementation.

Biting the cheek: Some people bite the delicate tissues in their cheeks or lips during sleep, or while chewing or talking. This is true especially for people who are suffering from TMJ or whose bite is uneven. This can result in lacerations and canker sores.

From ayurvedic point of view, people with high pitta in their saliva will have sharp teeth because the crown of the tooth becomes eroded. This can lead to repeated sores.

Foods: When you eat sharp, dried, or hard foods, such as popcorn, corn chips, crackers, or dried bread, it can hurt the oral mucous membrane resulting in canker sores. 

Hormonal imbalances

Viral infection

An underlying immunologic disease (such as HIV infection)

Trauma (such as that caused by biting the inside of the cheek or using a hard- bristled toothbrush)

Stress: Stress is often a precipitating factor in recurrent canker sores, suggesting a breakdown in normal immune function and/or integrity of the mucosal lining

Fatigue

Abnormal immune response to normal bacteria in the mouth

Canker sores are occasionally associated with Crohn's disease

Your sore persists for more than two weeks. This may indicate a more serious condition that needs treatment. A mouth ulcer that sticks around, even if it's not causing pain, could be the sign of oral cancer or a number of other disorders, including vitamin deficiency, anemia, or Crohn disease. 

You get sores once a week or more, especially when they appear in bunches.

Your canker sores are extremely painful; your doctor can give you medication to alleviate pain.

You have persistent multiple mouth sores, which may indicate an underlying problem, such as a drug reaction or, in rare cases, oral cancer or leukemia.