The purpose of this analysis is to study the clinical features, liver histology and the outcome after surgery in infants with choledochal cysts (CDCs), and to draw conclusions on the management strategy accordingly. The clinical features, liver histology and the outcome after surgery in 14 cases of CDCs treated before 1 year of age (the "infantile group") were compared with 52 cases that were diagnosed and treated between 1 and 12 years of age (the "classical pediatric group"). The differentiation of the "infantile choledochal cysts" from "biliary atresia with cystic dilatation" was based on the configuration of intrahepatic bile ducts on cholangiogram. Jaundice was the universal presenting feature in 14 patients in the "infantile group", the clinical presentation in 6 infants was indistinguishable from biliary atresia. On the other hand, pancreatitis as a presenting complication was seen exclusively in those presenting later, i.e. the "classical pediatric group". Fibrosis, as early as 4 weeks of age, was seen in all nine (100%) infants in whom a liver histology was available. Seven of these nine infants had bridging fibrosis (n = 4) or cirrhosis (n = 3) on liver histology. The outcome was satisfactory in 9 of the 14 (64.3%) infants despite bridging fibrosis (n = 4) or cirrhosis (n = 1) in 5 of these 9 babies. The CDCs presenting in infancy differ from the classical variety of later presenting pediatric CDCs in terms of their presentation, liver histology and outcome. They merit an emergent surgical treatment following which the outcome is satisfactory. Delay results in progression to end stage liver disease.