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Background The aim of this study was to assess the prevalence of biliary anatomical variants using 3-T MR cholangiography (MRC) with its impact in reduction of the complication of hepatobiliary surgical techniques. Results MRC was applied to 120 subjects (24 potential liver donors and 96 volunteers) and the right posterior hepatic duct insertion was documented, and accordingly, the biliary variants were classified based on Huang classification (Huang et al, Transplant Proc 28: 1669–1670, 1996). Biliary anatomic variants were divided based on Huang classification: Huang A1, 65.83% (n = 79); Huang A2, 11.67% (n = 14); Huang A3, 13.3% (n = 16); Huang A4, 7.5% (n = 9); and Huang A5, 1.67% (n = 2). The total frequency for A2, A3, A4, and A5 was 34.17% (n = 41). The distance between RPHD insertion and the junction of right and left hepatic ducts (L) was measured, and Huang A1 cases were then subtyped into S1 subtype (L > 1 cm) and S2 subtype (L ≤ 1 cm). We had 52 subjects with subtype S1 (43.33%) and 27 subjects with subtype S2 (22.5%). Twenty-three subjects had bile duct exploration or intraoperative cholangiograms and showed Huang type A1 in 14 (60.87%), type A2 in 3 (13.05%), and type A3 in 6 (26.08%). Twenty-two (95.65%) had the same classification in MRC and intraoperative while only one case (4.35%) was considered as A2 at MRC but the intraoperative classification was Huang A3, which was attributed to the insertion of the RPHD insertion at the distal end of the left hepatic duct. Conclusion MRC is an accurate tool for biliary tract mapping before hepatobiliary surgery to provide excellent identification of biliary variants which can reduce the incidence of biliary complications.