Objective To compare the medical outcomes of infants delivered by cesarean section with those of infants delivered vaginally. Methods A total of 301 healthy women with cesarean section and a matched control group of 301 women delivered vaginally were identified at three district-level hospitals in Shanghai from May 2001 to February 2003. Two groups were matched according to their medical indications for cesarean section. Their infants were assessed at delivery, 1 month, 6 month and 1 year after birth. Results The incidence of neonatal complications and infant morbidities at all measurement occasions did not differ significantly between groups. Rehospitalization was found to be more likely among infants delivered by cesarean section in the first month after birth. However, there was no difference between two groups in the incidence of rehospitalization in the first year after birth. Cesarean section was also associated with a higher risk of infant diarrhea (adjusted relative risk=1.25, 95% CI: 1.01, 1.56). Conclusion Infants did not have health benefits from cesarean section if the pregnancy was at low risk.