AimsBiliary intraductal tubular neoplasms that are non‐mucinous and negative for mucin 5AC (MUC5AC) are called intraductal tubulopapillary neoplasms (ITPNs). Intraductal tubular neoplasms with mucinous cytoplasm and MUC5AC positivity also occur and their nature remains unclear, although some pathologists may classify these as ‘intraductal papillary neoplasms of the bile duct (IPNBs) of gastric type’. This study aimed to elucidate genetic features of biliary intraductal tubular neoplasms.Methods and resultsSix resected cases of biliary intraductal neoplasm with >70% tubular configuration were characterised by clinicopathological examination and whole exome sequencing, and the findings obtained were compared between MUC5AC‐negative (n = 2) and ‐positive cases (n = 4). The intraductal tumours consisted of the pancreatobiliary‐type epithelium with high‐grade dysplasia arranged in back‐to‐back tubules. Both of the two MUC5AC‐negative cases were non‐invasive neoplasms and developed in the liver, whereas all MUC5AC‐positive cases had invasive carcinoma and were present in the intrahepatic (n = 2), perihilar (n = 1) and distal bile ducts (n = 1). In an exome‐sequencing study, MUC5AC‐negative cases harboured mutations in CTNNB1, SF3B1, BAP1 and BRCA1 (one case each). KRAS mutations were observed in three of four MUC5AC‐positive cases (75%) but none of the MUC5AC‐negative neoplasms. Compared to published data, known driver genes of other intraductal neoplasms of the pancreatobiliary system (e.g. APC, CTNNB1, STK11, GNAS and PIK3CA) were wild‐type in all but one MUC5AC‐negative case with CTNNB1 mutation. Chromatin modifiers (ARID1A, BAP1 and KMT2C) were also altered in MUC5AC‐positive cases, similar to usual cholangiocarcinomas.ConclusionsThis exome‐sequencing study suggested that MUC5AC‐negative biliary ITPNs are genetically distinct from pancreatic ITPNs and IPNBs. They may also biologically differ from MUC5AC‐positive tubular neoplasms despite morphological resemblance.