Salmonella infection. Gastrointestinal problems can arise from time to time in infancy. They are usually caused by a viral infection in the stomach. Rotavirus and Norwalk virus infection are common causes of gastroenteritis in babies and children. Escherichia coli , campylobacter, and salmonella are important bacterial causes of gastroenteritis. Some of the more common causes of gastrointestinal upset are described below, along with their symptoms and treatment. Rotavirus infection Rotavirus is the most common cause of a gastrointestinal upset and severe diarrhea in babies and children.