Causes of Diarrhea in Babies Diarrhea in babies is a common phenomenon, but many parents feel anxious and helpless when dealing with it, especially babies under one year old, because their immune systems are not mature enough and they are prone to bacterial infection. There are many reasons why babies have diarrhea. For example, it may be caused by eating unclean food or food allergies. Of course, it may also be caused by