Achieving an R0 resection can be difficult for hilar cholangiocarcinoma (HC) because of the anatomic structures of the hepatic hilum and frequent tumor infiltration. The aim of this study was to evaluate the margin status of bile duct resected in HC and prognostic impact of R1 resection. Between 2000 and 2009, 245 patients underwent operation for HC at Asan Medical Center. We retrospectively analyzed the clinicopathologic features and surgical outcomes, focusing on the proximal margin status, of 162 cases of patients with curative intention. Curative resections were achieved in 125 (52.1%) patients, and R1 resections were performed in 43 (26.5%). Proximal ductal margin states were classified as free margin (73.5%), carcinoma in situ (3.7%), and invasive carcinoma (22.8%). The 3- and 5-year survival rates of the R1 group (39.5% and 34.9%) were not significantly different from the rates of the R0 group (55.5% and 44.5%, respectively). Multivariate analysis showed lymph node metastasis (P = 0.001) and histologic differentiation (P = 0.001) were independent predictors of patient survival. The aggressive surgical approach based on liver resection including caudate lobe may increase the number of patients eligible for a curative chance and improve long-term survival even if the microscopically positive margin is still achieved.