Level 1: Causes of Baby Diarrhea Baby diarrhea is a matter of great concern to parents, and there may be many causes. First, it may be caused by improper diet. For example, if your baby eats too much food containing vegetable fiber or fruit fiber, or eats expired or stale food, it may cause gastrointestinal discomfort. Secondly, the baby may have diarrhea due to infection with viruses or bacteria.