Mucinous cystic neoplasm of the liver has been a controversial entity, in particular, regarding differentiation from intraductal papillary neoplasm of the bile duct. In this study, we compared the characteristics of hepatic mucinous cystic neoplasms with ovarian-like stroma (n=29) to those of cyst-forming intraductal papillary neoplasms of the bile duct (n=12). Radiological or macroscopic appearance, histological grade of malignancy, and postoperative clinical course were recorded. Immunohistochemistry for biliary or gastrointestinal markers was performed to characterize cell phenotypes. The patients with hepatic mucinous cystic neoplasm were all female and ranged in age from 21 to 67 years, which was significantly younger than that in the patients with biliary intraductal papillary neoplasm. Eighteen mucinous cystic neoplasms (76%) were located in the left lobe, with 13 (54%) in segment IV. Mucinous cystic neoplasms were significantly larger than intraductal papillary neoplasms (median diameter: 110 vs 50 mm, P=0.008). In contrast to intraductal papillary neoplasms that were all histologically malignant, 26 mucinous cystic neoplasms (90%) were adenomas, 2 (7%) were borderline malignant, and 1 (3%) was a carcinoma in situ. Benign mucinous cystadenomas had the pure biliary immunophenotype, whereas gastrointestinal markers including cytokeratin 20 and mucin core proteins 2, 5AC, and 6 were more frequently expressed in borderline or malignant mucinous cystic neoplasms and biliary intraductal papillary neoplasms. There was no mortality in the patients with mucinous cystic neoplasm, whereas one patient with intraductal papillary neoplasm died of cancer. In conclusion, hepatic mucinous cystic neoplasms and biliary intraductal papillary neoplasms have different clinicopathological characteristics as evidenced by differences in the age and gender of patients, macroscopic appearance, immunophenotypes, and grades of malignancy.