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Canker sores may also occur because of certain conditions and diseases, such as: 1  Celiac disease, a serious intestinal disorder caused by a sensitivity to gluten, a protein found in most grains. 2  Inflammatory bowel diseases, such as Crohn's disease and ulcerative colitis.
The vast majority of people who develop canker sores do not have another problem as the cause. 1  Both hereditary and environmental causes of the disease have been suggested, but the exact cause is not clear. 2  A number of factors have been suggested to precipitate outbreaks in susceptible individuals. 3  Oral trauma.