Epidermoid cysts of the biliary tree have not previously been described. A baby boy presented with a prenatally diagnosed echolucent intrahepatic cyst. Postnatal radioisotope study of the liver demonstrated that the cyst communicated with the biliary tree. Follow-up ultrasound at 6 months demonstrated that the cyst was filled with echogenic material consistent with either blood or biliary debris. Due to the potential for obstruction and cholangitis, surgery was planned. The cyst was located at the confluence of the right and left hepatic ducts and involved all of the common hepatic duct. The entire cyst was resected except for the patch containing 3 duct orifices: the opening of both hepatic ducts as well as the orifice leading to the common bile duct. A Roux-en-Y cyst jejunostomy was created to allow drainage of both left and right hepatic ducts. The connection also provided access to the cyst remnant through the common duct for future endoscopic monitoring of potential malignant transformation.