Intraductal papillary mucinous neoplasms of the biliary tract (BT-IPMNs) are unique but very rare biliary tumors. The relationship between BT-IPMNs and intraductal papillary mucinous neoplasm of the pancreas (P-IPMNs) was still unclear and controversial. We aimed to evaluate the clinical, radiological, histopathological, and prognostic characteristics of BT-IPMNs and P-IPMNs to achieve a better understanding of these two rare bilio-pancreatic diseases and their connections. Data of a total of 116 patients who were all surgically treated and histopathologically diagnosed as BT-IPMNs or P-IPMNs from January 2004 to December 2014 in our single institution was all retrospectively collected and analyzed. This study respectively enrolled 32 patients with BT-IPMNs and 84 ones with P-IPMNs. The differences between BT-IPMNs and P-IPMNs in age, sex ratios, clinical presentation, elevated tumor markers and proportion of malignancy were not statistically significant (P>0.05), while the tumor diameter of BT-IPMNs was notably smaller than P-IPMNs (1.72cm, 4.56cm, respectively; P=0.028). Patients with BT-IPMNs were more likely manifest the symptoms of cholangitis, compared to those with P-IPMNs who showed pancreatitis (75%, 30%, respectively; P=0.039). Bile duct dilatation (100%), tumor of bile duct cavity (50%) or/and cystic dilatation of the bile duct (50%) were the typical manifestations of preoperative imaging examinations of BT-IPMNs, in which tumors were mainly located in intrahepatic or hepatic hilar region (26, 81%). Surgery has been the curable treatment for BT-IPMNs in which left hepatic lobectomy was the most commonly performed procedure (20, 63%). Finally, compared with P-IPMNs, the overall mean survival time of patients with BT-IPMNs was a little shorter (59.1mon, 86.7mon, respectively; P=0.002). BT-IPMNs are a sort of rare and separate biliary tract neoplasm, which might be related with the stones of biliary tract or the infections of parasite. Although arising in different organs and representing different features, BT-IPMNs and P-IPMNs shared considerable clinical and pathological similarities which might represent related or similar development process in the bilio-pancreatic duct systems.