A 71-year-old woman, who had undergone laparoscopic cholecystectomy 1 year previously at our hospital, presented with abdominal pain, high fever, and jaundice. She was diagnosed with choledochal stenosis caused by migration of the clips that were used at the previous operation. At reoperation, the common bile duct was successfully dissected, including the stenotic site, where a metal clip was found to be penetrating the duct wall. The stenotic site was sufficiently resected, when a black-brown gallstone was found proximally to the stenosis. Interestingly, the stone was found to contain two metal clips, which were considered to have migrated into the bile duct and to have acted as a nidus for stone formation. The common bile duct was reconstructed by direct end-to-end anastomosis. Surgeons must exercise caution in the use of metal clips, keeping in mind the potential risk of clip migration.