BackgroundInformation on rare hepatobiliary and pancreatic (HBP) subtypes of cancer is scarce. We aimed to elucidate the incidence and clinical features of rare tumors in Japan using the National Cancer Registry (NCR), a new nationwide integrated population-based registry.MethodsThe data of patients diagnosed in 2016–2017 were extracted from the NCR database, and classified by topography: liver cells, intrahepatic bile duct, gallbladder, extrahepatic bile duct, ampulla of Vater, and pancreas. Data were described and analyzed using the World Health Organization and General Rules tumor classifications. The incidences for all rare tumors including hepatoblastoma and adenosquamous cell carcinoma were calculated as the number of new cases divided by the corresponding total person years.ResultsThe NCR data yielded 8,239 patients with rare HBP tumors between 2016 and 2017. The ratios of rare tumors to all cancer types were 0.5%, 0.7%, 3.9%, 1.6%, 0.8%, and 7.2% in the liver, intrahepatic bile duct, gallbladder, extrahepatic bile duct, ampulla of Vater, and pancreas, respectively. Rare tumors occurred more frequently in men, except for gallbladder tumors. The main tumor stage was localized in liver cells (42.4%) and the intrahepatic bile duct (51.6%); more patients were diagnosed in advanced stage with gallbladder (84.1%) and extrahepatic bile duct (74.4%) tumors. Approximately equal percentage of patients were diagnosed at designated cancer care hospitals (DCCHs) and non-DCCHs, whereas 60% to 70% patients received treatment at DCCHs.ConclusionThis is the first report to provide comprehensive information on the epidemiological status of rare HBP tumors in Japan by utilizing population-based NCR data.