Magnetic resonance (MR) imaging plays an important role in the preoperative evaluation of the living-related liver donors to reduce postoperative morbidity and complications. Though invasive, intraoperative cholangiography is still the golden standard in demonstrating anatomical variation of bile ducts. We design this study to compare the validity and reliability between these two imaging modalities and retrospectively searched the database of living-related liver transplantation (LRLT) center during the period from April 2005 to September 2008. The clinical information and images of total 58 donors (female : male = 35 : 23) were reviewed. Five types of branching patterns of the bile ducts were encountered. The rate of disagreement in the classification of branching pattern between MR and intraoperative cholangiography was 5% (3/58). Intraoperative cholangiography could detect significantly more division degree of right hepatic ducts (mean degree: 7) than MR cholangiography (mean degree: 4) (using paired t-test, p < 0.05). No significant difference existed in the detection of division degree of left hepatic ducts. However, MR cholangiography was significantly better than intraoperative cholangiography in demonstrating major branches of the left hepatic ducts including tributaries of segment 2 and 3 (58/58 versus 35/58) (using McNemar's chi-square test, p < 0.05). We conclude that MR cholangiography is nearly as good as intraoperative cholangiography in identifying the branching pattern of bile ducts, and demonstrates the major left hepatic ducts better.