OBJECTIVE The aim of this study was to compare prospectively the diagnostic efficacy of magnetic resonance (MR) imaging and endoscopic ultrasonography (EUS) in extrahepatic biliary obstruction. METHODS A total of 50 patients with suspected benign or malignant extrahepatic biliary obstruction underwent MR imaging, including MR cholangiopancreatography, and EUS, within a median time delay of 1 day. The final diagnosis was established by endoscopic retrograde cholangiopancreatography in 37 cases, intraoperative cholangiography in nine cases, and clinical and biochemical follow-up in four cases. RESULTS In total, 33 patients had extrahepatic biliary obstruction, of benign origin in 21 cases and of malignant origin in 12 cases, whereas 17 had no evidence of obstruction. The sensitivity and specificity of MR imaging were 91% and 94 %, respectively. There were one false-positive and three false-negative results, all related to choledochal sludge. The corresponding values for EUS were 97% and 88%. There were two false-positive results and one false-negative result. False-positive diagnoses were related to the presumed presence of biliary sludge and choledocholithiasis, whereas the false-negative diagnosis occurred in one patient with a final diagnosis of sludge. No significant difference in sensitivity and specificity was observed between the two imaging methods (P>0.05). CONCLUSIONS In our study MR imaging was as accurate as EUS in the diagnosis of extrahepatic biliary obstruction.