1. What causes mucus in baby’s stool? Mucus in your baby\’s stool can be caused by a variety of reasons. First, your baby\’s digestion is not fully developed yet, so if breast milk or formula contains too much lactose or protein, it may cause mucus in the stool. Secondly, if your baby is growing, excessive food intake can also lead to mucus in the stool. In addition, infections, allergies, and