PURPOSE: Even after excision of choledochal cyst, late postoperative complications can develop. This study was conducted to examine the long-term outcome of cyst excision. METHODS: Of 50 choledochal cysts treated over a 10-year period (1991~2000), excluding cancer and rare types, 39 patients (type I: 21, IVa: 18) who underwent cyst excision were reviewed to evaluate the late outcome. RESULTS: Median follow-up period was 24 months after surgery. Late complications (5 intrahepatic duct stone, 4 cholangitis, 4 pancreatitis, and 1 malignancy) developed in 14 (35.9%) patients. Of the 5 patients with intrahepatic duct stone, 2 underwent choledochoscopic stone removal, one of whom additionally underwent balloon dilatation for anastomotic stricture. The remaining 3 patients were free of symptoms and didn't need further management. Of the 4 patients with cholangitis, one underwent left lateral sectionectomy for remaining intrahe patic cyst in type IVa and another patient balloon dilatation for anastomotic stricture. The remaining 2 patients developed cholangitis because of incomplete excision and ascending cholangitis, and they were conservatively managed. Of the 4 patients with pancreatitis, 2 developed pancreatitis because of pancreas divisum and probably residual distal cyst. The symptoms of all four patients with pancreatitis were mild and treated with conservative management. Periampullary cancer developed 18 months after cyst excision in one patient. CONCLUSION: To minimize hepatopancreatobiliary complications and malignancy after cyst excision, complete excision of the extrahepatic bile duct should be performed. Moreover, long-term follow-up is necessary because of these late complications.