We report herein an extremely rare complication; namely, endo-clip migration into the common bile duct, following laparoscopic cholecystectomy, that occurred in a 57-year-old man. He underwent laparoscopic cholecystectomy, but postoperative bile leakage occurred from the cystic duct stump and he was treated by conservative drainage for 1 month. Five years later, he complained of vomiting and pain in the right hypochondrium, and he was admitted for investigations of jaundice and liver dysfunction. Computerized tomography scanning of the abdomen and endoscopic retrograde cholangiography revealed that several calculi, with six endo-clips as nuclei, had migrated into the biliary tract. Endoscopic removal of the calculi following endoscopic sphincterotomy, using a basket catheter, was unsuccessful, and it was therefore necessary to remove the basket catheter surgically. The mechanism of endo-clip migration and the method for removing the endo-clips are briefly discussed.