This analysis was undertaken to compare the clinicopathological features of infants with choledochal cysts to those of older children with these entities and to evaluate the surgical outcomes for both subject groups. The medical records of all children admitted to the Cathay General Hospital with choledochal cysts over a 20-year period were retrospectively reviewed. Twenty-five subjects were included and divided into the infant (<1 year at presentation; 8 subjects) and classical pediatric (1-18 years at presentation; 17 subjects) groups. Anatomical subtypes were: IA (16), IC (6), and IVA (3). The median biliary amylase value was markedly elevated for the pediatric group but not for the infant group. Most (82.4%) patients in the pediatric group, but none in the infant group, presented with abdominal pain. Jaundice and clay-colored stool were present in all patients in the infant group but only 35% of those in the pediatric group. All patients underwent choledochocystectomy and Roux-en-Y hepaticojejunostomy with good outcomes. Neonates/infants with choledochal cysts present differently from older children with these entities. Amylase measurements may serve to distinguish biliary atresia with cystic dilatation from choledochal cyst in neonates/infants. Prognosis following radical cyst excision and reconstruction with Roux-en-Y hepaticojejunostomy is excellent.