A 58-year-old man on abdominal ultrasonography and CT had an irregularly elevated lesion at the neck of the gallbladder and a cyst of approximately 6.5 cm in diameter at the pancreatic tail. Percutaneous transhepatic cholangiography revealed a 2-cm shadow defect at the neck of the gallbladder and an irregular, translucent 30 x 12 mm lesion in the intrapancreatic bile duct. Total pancreatectomy and extended cholecystectomy with regional lymph node dissection was performed. An anomalous arrangement of the pancreaticobiliary ductal system (AAPBD) was demonstrated by postoperative contrast radiography of resected specimen. The lesions of the gallbladder and common bile duct were papillary adenocarcinoma. In addition, papillary adenocarcinoma was limited almost entirely to the mucosal layer of the main pancreatic duct and its branches, from the junction of the common bile duct and pancreatic duct to the pancreatic tail. The three tumors were not continuous. The cyst at the pancreatic tail was a pseudocyst. This case represents synchronous cancer of the gallbladder, common bile duct, and pancreas associated with AAPBD.