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We report here on a case of intraductal papillary mucinous neoplasm (IPMN) of the bile duct, associated with gallbladder agenesis. A 65-year-old woman was admitted to the hospital with epigastric pain, anorexia, and nausea. Abdominal computed tomography scan and magnetic resonance imaging showed a 5×2.5 cm lobulated cystic lesion in the lateral lobe of the liver. The gallbladder was not seen on both imaging modalities. Endoscopic retrograde cholangiopancreatography suggested the diagnosis of biliary IPMN due to abundant mucin that protruded from the papilla and the lobulated cystic lesion. Laparoscopic wedge resection of the liver was performed. The final pathology was consistent with biliary IPMN. The specimen showed multifocal high-grade dysplasia with negative resection margins. The patient experienced no postoperative complications and was discharged 5 days after the operation.