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Aphthous stomatitis (canker sores, aphthous ulcers) is the name given to those painful and annoying sores that appear in the mouth, often in the area between the gum and the cheek. They unfortunately tend to recur; there may be some tendency for these sores to be familial. Recurrent aphthous ulcers can also be associated with systemic disease, including inflammatory bowel disease (especially Crohn disease) and several other syndromes.
When I was in medical school, it was unknown exactly what causes these lesions nor was there any really effective therapy available. That is still pretty much the status quo (although the theory is that they are caused by an alteration in the local immune system of the oral mucous membrane, brought on by various stresses). Pain relief with something like Oragel® is usually about all we can offer the small child. Older children can swish and spit viscous lidocaine (a prescription medication). A topical corticosteroid in a sticky base (0.1% triamcinolone in Orabase®) may help to reduce inflammation. (See the more general discussion of stomatitis.)