In this study, CA19-9 and CA125 in serum and bile were measured to evaluate their diagnostic value in cholangitis and bile duct carcinoma. Patients were classified into three groups: group A, the control group, had cholelithiasis without infection (n = 23), group B had acute cholangitis (n = 25) and group C had bile duct carcinoma without bacterial infection (n = 18). All patients had undergone surgery, and bile and serum of the patients were measured for the two tumour markers by radio-immunoassay. The positivity rate for serum CA19-9 was 4.4% in the control group, 28.0% in group B and 61.1% in group C. The positivity rates for serum CA125 in groups control, B and C were 0%, 4% and 27.78% respectively. The diagnostic accuracy for bile duct carcinoma was 67.4% for both CA19-9 or CA125. The concentration of CA19-9 in bile was more than 1200 ng/mL in 72% of patients with acute cholangitis, in 61.1% of all patients with bile duct carcinoma and 0% in the control group. The frequency of concentrations of CA125 in bile greater than 200 ng/mL was 38.89% in bile duct carcinoma and none was observed in the control or acute cholangitis groups. In conclusion, the concentration of CA19-9 was increased not only by the tumour itself, but also by infection. In the diagnosis of bile duct carcinomas, the sensitivity of CA125 was low but its specificity was very high.