Mouth ulcers can sometimes be caused by certain medical conditions, such as: viral infections – including the cold sore virus, chickenpox, and hand, foot and mouth disease. vitamin B12 or iron deficiency. Crohn's disease – a long-term condition that causes inflammation of the lining of the digestive system. Mouth ulcers can be caused by a wide range of factors including: accidental biting of the inside of your cheek. injury from a toothbrush (such as slipping while brushing) constant rubbing against misaligned or sharp teeth. constant rubbing against dentures or braces. poor oral hygiene. burns from eating hot food.