SOX9 is an important transcription factor required for development and has been implicated in several types of malignant tumor. Our recent study showed that SOX9 played an important role in multi-step carcinogenesis in cases of intraductal papillary mucinous tumor of the pancreas (IPMN-P). This study aimed to investigate the expression of SOX9 in cases of intraductal papillary mucinous tumor of the bile duct (IPMN-B).SOX9 expression was immunohistochemically evaluated in the tumor and corresponding normal bile-duct epithelium of seven IPMN-B patients.In all cases, SOX9 expression in the IPMN-B was low compared with the normal biliary epithelium.This study demonstrated that SOX9 expression may indicate a link between IPMN-B and IPMN-P. SOX9 may also have potential as a therapeutic target and/or prognostic marker in IPMN-B.