The most common cause of diarrhea in babies and young children is viral gastroenteritis — the garden-variety stomach bug. Rotavirus used to be the dominant culprit, but widespread vaccination has dramatically reduced severe rotavirus cases. Norovirus has picked up some of the slack, and it is notoriously contagious. If one family member gets it, the odds of the whole household going down are substantial.
Viral gastroenteritis typically starts with vomiting, which tapers off after one to two days, followed by watery diarrhea that can last three to seven days. There may be a low-grade fever. The illness is self-limiting, meaning it resolves on its own — the primary concern is keeping your baby hydrated while their body fights off the virus.
Antibiotic-associated diarrhea is the second most common scenario. When your baby takes antibiotics for an ear infection or other bacterial illness, the medication does not discriminate between good and bad bacteria. It disrupts the gut microbiome, and diarrhea often follows within a few days of starting the medication. This usually resolves after the antibiotic course ends, as the gut bacteria repopulate. Some pediatricians recommend probiotics during antibiotic use, though the evidence is mixed.
Food sensitivities are another frequent cause, with cow's milk protein allergy (CMPA) being the most significant. CMPA affects approximately two to three percent of infants and can cause chronic diarrhea, often with mucus or blood streaks. If your baby has persistent loose stools along with other symptoms like eczema, excessive fussiness, or blood in the diaper, CMPA should be on the radar. See our milk protein allergy guide for a deeper look.
Then there is the teething question. Parents have been attributing diarrhea to teething for generations, and the reality is more nuanced than either "teething causes diarrhea" or "it definitely doesn't." Research does not support a direct physiological link between tooth eruption and diarrhea. However, teething babies drool excessively and put everything in their mouths, which increases their exposure to pathogens. So the loose stools that coincide with teething may be caused by something the baby picked up while gnawing on a shopping cart handle, not by the tooth itself.