Duplication of the cystic duct is a rare variation of the biliary system. It is important to pay attention to this variation to avoid intraoperative biliary system injury, especially during laparoscopic cholecystectomy. In a 66-year-old woman with gallstones, endoscopic retrograde cholangiopancreatography (ERCP) revealed no anomaly of the biliary system. At laparoscopic cholecystectomy, although intraoperative cholangiography demonstrated the second cystic duct, we misdiagnosed the duplication of cystic duct because preoperative ERCP had demonstrated normal anatomy. It was thought that the second cystic duct was dissected during the operation and the patient suffered from postoperative bile leakage. After reoperation, the patient recovered well. The diagnostic and therapeutic problems of such an anomaly are discussed below with the review of the literature.