BACKGROUND Choledochal cyst is an uncommon congenital disease of the biliary tract in the UK. There are five main types of choledochal cyst with several recognised sub-types. However, occasional variants do occur. METHODS We report a case of a female infant with an antenatally diagnosed choledochal cyst. The operative cholangiogram revealed an unusual intrahepatic biliary tree. The cyst was successfully excised and the infant is well at 18-months follow up. CONCLUSIONS The anatomy should be clearly defined before surgical excision as abnormal variants can occur, which usually do not fit into the known classification types and subtypes.