This study aimed to investigate the clinical utility of Duke pancreatic monoclonal antigen type 2 (DUPAN-2) in addition to carbohydrate antigen 19-9 (CA19-9) and carcinoembryonic Antigen (CEA) in biliary tract cancers (BTCs). Patients who underwent surgery for BTC were investigated. BTCs included five types: intrahepatic cholangiocarcinoma (ICC), hilar cholangiocarcinoma (HC), distal cholangiocarcinoma (DC), gall bladder carcinoma (GBC), and ampullary carcinoma (AC). The percentages of patients with elevated and normal tumor marker levels (high and normal groups) were determined across five BTC types, and recurrence-free survivals (RFSs) were compared between the two groups. Forty, 67, 56, 51, and 51 patients had ICC, HC, DC, GBC, and AC, respectively. In all patients, the percentages of patients with elevated tumor marker levels decreased in the order of CA19-9 (44.9%), DUPAN-2 (36.6%), and CEA (17.0%). This trend was consistent across four cancer types: ICC, HC, DC and GBC. In all patients, the high groups in three markers exhibited significantly poorer RFSs compared to the normal groups (P < 0.01, P < 0.01, P < 0.01, respectively). DUPAN-2 is a useful marker for recurrence in patients with resectable BTC.