Hilar cholangiocarcinoma (HCCA), which lacks specific clinical manifestations, remains very difficult to distinguish from benign disease. This distinction is further complicated by the complex hilar anatomy. We conducted the present study to evaluate the differential diagnosis of these conditions. Sixty-five patients underwent resection surgery for suspected HCCA between January 2011 and October 2018. Institutional Review Board of Shengjing hospital agreed this study and all participants sign an informed consent document prior to participation in a research study. Following a postoperative pathology analysis, all patients were divided into two groups: malignant group (54 patients with HCCA) and benign group (11 cases with benign lesions). Compared with the benign group, the malignant group had a significantly higher median age and serum CA19-9, CEA, ALT, BILT and BILD levels (P < 0.05). In contrast, the groups did not differ significantly in terms of the sex distribution, clinical manifestations, serum levels of AST and ALKP, and imaging findings. In a receiver operating characteristic curve analysis, we identified a CA19-9 cutoff point of 233.15 U/ml for the differential diagnosis and CEA cutoff point of 2.98 ng/ml for the differential diagnosis. The differential diagnosis of HCCA and benign hilar lesions remains difficult. However, we found that patients with HCCA tended to have an older age at onset and higher serum levels of CA19-9, CEA, BILT, ALT and BILD. Furthermore, patients with a serum CA19-9 level >233.15 U/ml and CEA level >2.98 ng/ml are more likely to have malignant disease.