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Surgical clip migration and subsequent stone formation in the common bile duct is a rare but well-established complication after laparoscopic cholecystectomy. There are some suggestions about the mechanisms of the migration process, but the details are still unclear. We report here a case in which common bile duct stones were formed around surgical clips, and other clips were found to have penetrated into the common hepatic duct, which we believe were in the process of migration after laparoscopic cholecystectomy. The patient required a laparotomy to retrieve the bile duct stones due to the distal stricture, and another laparotomy was necessary to remove the penetrating clips, which were deeply embedded in the bile duct wall. Although a variety of endoscopic and percutaneous interventional procedures are available in this era of modern medical technology, it is sometimes impractical to apply these procedures in such cases as ours, and exploratory laparotomy is sometimes required to correctly treat the patient. This case shows that the metallic surgical clips can penetrate into the intact bile duct wall through serial maceration, and we believe that careful application of clips may be the only way to prevent their migration after laparoscopic cholecystectomy.