In most cases of congenital cyst of the extrahepatic biliary system, a single choledochal cyst is described. We have reported a patient with multiple intrahepatic and extrahepatic biliary cysts. Intraoperative cholangiograms demonstrated free reflux among the multiple choledochal cysts, with reflux into the intrahepatic biliary ductal system. After a side-to-side choledochocystoduodenostomy, the patient recovered and has remained asymptomatic for over a year.