1. Reasons why babies have green stools. Baby’s green stools may be caused by indigestion, intestinal infection, allergic reactions, etc. Indigestion may be due to a poor diet or immature digestion; intestinal infections may be caused by bacterial or viral infections; and allergic reactions may be due to a food allergy. 2. How to deal with your baby’s green stool. To deal with your baby’s green stool, you first need to find the cause, and then