The aim of this study is to evaluate the prognostic impact of an intraductal carcinoma component and bile duct resection margin status in patients with biliary tract carcinoma. An intraductal carcinoma component was defined as carcinoma within the bile duct outside the main tumor nodule consisting of a subepithelial invasive component. Surgically resected materials from 214 patients were evaluated by histological observations. Seventy-nine patients (36.9%) with an intraductal carcinoma component infrequently developed large tumors and infrequently showed deep invasion and venous, lymphatic and perineural involvement in the main tumor nodule. An intraductal carcinoma component was inversely correlated with advanced clinical stage, and was shown to be a significantly favorable prognostic factor by both univariate and multivariate analyses. Proximal (hepatic) side bile duct resection margin status was categorized into negative for tumor cells, positive with only an intraductal carcinoma component [R1 (is)], and positive with a subepithelial invasive component (R1). Forty-five patients (21.0%) with an R1 resection margin had a poorer prognosis than 148 patients (69.2%) with a negative resection margin, whereas 21 patients (9.8%) with an R1 (is) resection margin did not. In patients with an R1 resection margin, the risk of anastomotic recurrence was higher, and the period until anastomotic recurrence was shorter, than in patients with an R1 (is) resection margin. Surgeons should not be persistent in trying to achieve a negative surgical margin when the intraoperative frozen section diagnosis is R1 (is), and can choose a safe surgical procedure to avoid postoperative complications.