The purpose of this study was to compare the efficacy of MR cholangiopancreatography (MRCP) and endoscopic retrograde cholangiopancreatography (ERCP) for the diagnosis of intrahepatic stones. Of the 318 patients who underwent MRCP examinations at our institution during an 18-month period, we identified 49 patients who subsequently underwent surgery or cholangioscopic stone removal with proof of intrahepatic stones. Thirty-four of these patients also underwent ERCP; they made up our study population. All images were interpreted for the presence of bile duct stones: MRCP images were interpreted independently by two reviewers, and ERCP studies were interpreted by one reviewer who was unaware of the MRCP findings. The sensitivity and specificity of MRCP for detecting intrahepatic stones were 97% and 93%, respectively, whereas those of ERCP were 59% and 97%, respectively. MRCP showed a significantly higher sensitivity than ERCP in the diagnosis of intrahepatic stones (p < 0.001). We found no significant difference between MRCP and ERCP in sensitivity or specificity for detecting calculi in the common duct or gallbladder. MRCP is a more effective diagnostic method than ERCP for the evaluation of intrahepatic stones.