Background Few reports have evaluated the efficacy of re-operation for relapse after injtial surgery for hepatocellularcarcinoma (HCC) with bile duct thrombosis (BDT). The aim of this study was to investigate the efficacy of initial surgeryand subsequent re-operation for HCC with BDT, and their effects on prognosis.Methods The clinical data of 880 patients with HCC, including 28 patients with BDT, who underwent radicalhepatectomy between 1998 and 2008 in our hospital, were reviewed. The effects of BDT and re-operation on prognosiswere retrospectively analyzed.Results The 1-, 3- and 5-year survival rates were 89.3%, 46.4% and 21.4%, respectively, in 28 patients with BDTversus 91.4%, 52.9% and 20.9% in 852 patients without BDT (P>0.05). Six patients with BDT underwent re-operationafter disease relapse, and their survival time was significantly longer than those who did not undergo re-operation (P<0.05). Multivariate analysis indicated that portal vein invasion and tumor size were independently associated with tumorrelapse and prognosis (P<0.05). Univariate analysis and multivariate analyses showed that obstructive jaundice was notsignificantly correlated with tumor relapse or prognosis (P>0.05).Conclusions Hepatectomy plus BDT removal is an effective treatment option for HCC with BDT. Obstructive jaundiceis not a contraindication for surgery. Re-operation after relapse can provide good outcomes if the cases are appropriatelyselected.