Intraductal papillary epithelial neoplasms of the pancreatobiliary system (intraductal papillary neoplasm of the bile duct (IPNB) and intraductal papillary mucinous neoplasm (IPMN)) seem to share many clinicopathological features; however, IPNB has not been fully characterized. In order to understand the clinicopathological/immunohistochemical features of IPNB better, we compared 52 cases of IPNB with 42 cases of IPMNs with mural nodules. The IPNB cases were divided into two groups according to their histological similarity and according to five key histological findings. All IPNB and IPMN cases mainly affected middle-aged to elderly people, predominantly men. Mucin hypersecretion was less frequent in IPNB compared to IPMN. Group 2 IPNB more frequently had a higher histopathological grade and more extensive stromal invasion than IPMN. Group 1 IPNB and IPMN were further classified into four subtypes (gastric, intestinal, pancreatobiliary, and oncocytic). Although each subtype of IPNB and IPMN showed similar histology, the immunohistochemical results were different. The gastric type of IPNB was less frequently positive for CDX2, and intestinal IPNB was more frequently positive for MUC1 and less frequently positive for MUC2, MUC5AC, and CDX2 compared to each subtype of IPMN, respectively. In conclusion, IPNB and IPMN have some clinicopathological features in common, but mucin hypersecretion was less frequent both in IPNBs than in IPMN. Group 2 IPNB differed from IPMN in several parameters of tumor aggressiveness. Additional clinicopathological and molecular studies should be performed with respect to the subtypes of IPNB and IPMN.