Cyst excision and biliary diversion are generally accepted operative procedures for choledochal cysts to prevent biliary tract carcinoma. We report herein a case of carcinoma of the hepatic hilus developing in the hepatic hilus 21 years after biliary diversion for a choledochal cyst. A 62-year-old female was admitted to our hospital because of refractory cholangitis. A diagnosis of carcinoma of the hepatic hilus was made based on a cholangiogram, biliary fiberscopy and biopsy. She underwent a curative resection of the tumor. Biliary tract carcinoma may be a late postoperative complications of choledochal cysts. Long-term follow-up of the patient is necessary after the primary operation.