Causes of Canker Sores are following:

• Canker sores do not appear to be caused by viruses or bacteria, although an allergy to a type of bacterium commonly found in the mouth may trigger them in some people.

• Canker sores occur along with gastrointestinal problems, such as an inability to digest certain cereals

• Some studies have shown a connection with toothpaste containing sodium lauryl sulfate in some individuals. Try 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.

• 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. Vitamin C deficiency has also been associated with canker sores.
• Spicy and/or acidic foods often produce a canker sore as a response to the irritation these spices and acids create in the mouth.
• Canker sores often run in families. Genetics my be a factor for many canker sore sufferers
• Emotional stress and local trauma or injury to the mouth can lead to canker sores.