The present study aimed to identify the pathologic and genetic characteristics of intestinal subtype of intraductal papillary neoplasm of the bile duct (iIPNB) showing columnar cells with pseudostratified, cigar-shaped nuclei, and basophilic or amphophilic cytoplasm with the diffuse immunohistochemical expression of CK20 and/or CDX2. A total of 34 cases of iIPNB were pathologically examined according to their anatomic location (the bile duct) and were then compared with the intestinal subtype of intraductal papillary mucinous neoplasm (iIPMN) of the pancreas (n=22). Mutations of 26 somatic genes were examined in formalin-fixed paraffin-embedded tissue specimens from 21 cases of iIPNB using the TruSight Tumor 26 gene panel and next-generation sequencing. iIPNB cases were divided into intrahepatic (n=6) and extrahepatic (n=28) categories. Intrahepatic IPNBs showed a less-complicated villous-papillary pattern, while extrahepatic IPNBs showed a papillary pattern with tubular and/or villous components and predominant high-grade dysplasia with complicated architectures. MUC5AC was frequently and extensively expressed in intrahepatic iIPNBs and iIPMNs but not in extrahepatic iIPNBs. CD10 was frequently expressed in extrahepatic IPNBs but not in intrahepatic iIPNBs or iIPMN. Genetic mutations of TP53 and PIK3CA, which were infrequent or absent in iIPMNs, were frequently detected in extrahepatic iIPNBs, while KRAS and GNAS, which were commonly observed in iIPMNs, were frequently detected in intrahepatic iIPNBs. Intrahepatic iIPNBs showed villous-papillary growth with features reminiscent of iIPMNs, while extrahepatic iIPNBs showed papillary growth with tubular and/or villous components, complicated histology and variable differences from iIPMNs, suggesting differences in the tumorigenesis of iIPNBs along the biliary tree.