1. Causes of diarrhea in babies There are many causes of diarrhea in babies, which may be indigestion, infectious diarrhea, allergies, etc. Indigestion is caused by eating too much or too little food, poor quality food, or eating too fast. Infectious diarrhea is caused by bacteria, viruses, etc., such as rotavirus, E. coli, etc. Allergy is due to