A case of mucinous biliary cystadenoma with mesenchymal stroma (CMS tumor) in a 64-year-old woman is reported. The patient presented with acute abdominal pain and a palpable mass in the upper abdomen. Computed tomography and abdominal sonography showed characteristic multilocular cysts in the left lobe of the liver. Serum CA 19-9 was elevated to 108 U/ml with normal carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP) levels. The levels of CA 19-9 and CEA in the cystic fluid were high at 7430 U/ml and 576 ng/ml, respectively. The serum CA 19-9 returned to 35 U/ml 4 weeks after tumor resection. These corresponding findings of both tumor markers in the serum and cystic fluid imply that (1) CA 19-9 and CEA both exist in the epithelial component of CMS tumors as evidenced by immunohistochemical stain, (2) serum CA 19-9 is a valuable marker in the diagnosis and monitoring of CMS, and (3) in cystic fluid, there are more significantly high levels of CA 19-9 in CMS compared with levels in simple cyst and polycystic liver disease. Therefore, measurement of CA 19-9 in cystic fluid and serum may be helpful in the differential diagnosis of hepatic cystic lesions.