To compare the diagnostic performance of magnetic resonance (MR) imaging and multidetector row computed tomography (MDCT) for an anomalous pancreaticobiliary ductal junction (PBJ). This study included 26 patients who underwent MR imaging, MDCT, and endoscopic retrograde cholangiopancreatography. Seventeen of the patients were diagnosed by endoscopic retrograde cholangiopancreatography as having an anomalous PBJ. Three radiologists independently reviewed MR images alone, contrast-enhanced CT images alone, and MR images and CT images combined. Receiver operating characteristic curve analysis was used to compare diagnostic capabilities. The mean area under the receiver operating characteristic curve (Az [95% confidence interval]) was 0.75 (0.73-0.77) for MR imaging alone, 0.79 (0.70-0.89) for CT alone, and 0.84 (0.82-0.86) for the 2 modalities combined. Only between the combination and MR imaging alone was there significant difference in Az value (P < 0.05). The diagnostic performance of MR imaging and MDCT was equivalent for an anomalous PBJ. The addition of MDCT to MR imaging improved the diagnostic performance.