Background: The clinical relevance of the ductal margins in operative resection of bile duct carcinoma has not been well established. The purpose of this study was to assess the prognostic significance of ductal margins in patients with bile duct carcinoma. Method: A total of 256 patients with bile duct carcinoma were analyzed retrospectively. We compared clinicopathologic features, outcomes, and recurrences among patients who underwent curative resections with free margins (D-FRE: n = 185), noncurative resections only resulting from the involvement of ductal margins with carcinoma in situ (D-CIS: n = 13), noncurative resections only caused by the involvement of ductal margins with invasive foci of carcinoma (D-INV: n = 17), and noncurative resections resulting from any other margin state and/or distant metastases (OTH: n = 41). Results: Histologic grades, node involvements, T classifications, and JSBS staging were significantly associated with the ductal margin state. The 5-year survival rate by Kaplan-Meier analysis was 54.7%, 52.4%, 17.6%, and 16.7% for patients with D-FRE, D-CIS, D-INV, and OTH, respectively. A multivariate analysis by the Cox proportional hazards model has shown that, in addition to lymph node involvement (P = 6.6 × 10-4) and venous invasion (P = 2 × 10-5), D-FRE versus D-INV and D-FRE versus OTH, but not D-FRE versus D-CIS, were independently associated with survival with P values of 8 × 10-4 and 1.4 × 10-5, respectively. Taken together along with the difference in the recurrence rates, patients with D-CIS seem to have outcomes similar to D-FRE but different from D-INV or OTH. Conclusion: Compared with free ductal margins, the ductal margins with invasive foci of carcinoma may involve a significant disadvantage in terms of patients' outcomes in surgical resection for bile duct carcinoma, unlike those with carcinoma in situ.