Many causes. The cause of canker sores is not well understood. More than one cause is likely, even for individual patients. 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. The sores may be an allergic reaction to certain foods. In addition, your own immune system can cause them.
Depends on cause. Aphthous stomatitis involving the common canker sore can occur in up to 15% of americans, and may involve some bacteria like staph epidermidis. However, similar-appearing aphthous ulcers can be seen with herpes, crohn's disease, and other systemic disorders, if you have multiple aphthous ulcers or frequently recurring ones please have the lesions checked out.