Stool malodor in babies may be protein allergy, it may also be related to indigestion, acute enteritis, lactose intolerance and so on. 1. Indigestion: If the baby has consumed too much protein or sugary food, which cannot be fully digested by itself, it may cause the food to stay in the intestines for a long time and ferment, so there is foul-smelling stools. 2. Acute enteritis: If the baby has acute enteritis, it may also cause the food to ferment in the intestines and produce too much gas, so there is a situation of smelly stools. 3. Lactose intolerance and food protein allergy: If the baby is lactose intolerant or allergic to food protein, the protein may ferment in the intestinal tract, resulting in smelly stools. As you can see, there are many reasons why a baby’s stool smells bad, so you should consult a doctor according to your child’s specific situation and give him or her the right treatment under the doctor’s guidance.