In a multivariable model using MMP-9 (cut-off value = 15 ng/ml), MMP-7 (cut-off value = 7.4 ng/ml), CEA (cut-off value = 5 ng/ml), CA19-9 (cut-off value = 100 U/ml), MMP-9 (an adjusted odds ratio = 3.76; 95% CI = 1.05–13.47; p = 0.04), MMP-7 (an adjusted odds ratio = 5.33; 95% CI = 1.55–18.31; p = 0.008) and CA19-9 (an adjusted odds ratio = 4.60; 95% CI = 1.23–17.30; p = 0.02) were the independent predictors of cholangiocarcinoma, whereas CEA was not. The gene discussed is MMP7; the disease is cholangiocarcinoma.