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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.
What causes canker sores? No one knows what causes canker sores. The vast majority of people who develop canker sores do not have another problem as the cause. Both hereditary and environmental causes of the disease have been suggested, but the exact cause is not clear. A number of factors have been suggested to precipitate outbreaks in susceptible individuals.