Developments in magnetic resonance (MR) equipment and techniques have been remarkable. Especially, respiratory-triggered three-dimensional MR cholangiopancreatography (3D-MRCP) has been developed to provide images with high spatial resolution of the biliary tract and pancreatic duct. These 3D data can be employed in MR virtual endoscopy (MRVE) with volume rendering to visualize the lumina of the gallbladder, bile duct, and pancreatic duct. To observe the changes in the lumina with threshold settings on a workstation, we made an original phantom with tubes 2, 3, and 6 mm in internal diameter. We examined the changes in luminal diameter using several threshold settings by comparing the actual internal diameters to determine an appropriate threshold setting, which we then applied in 50 clinical cases, including pancreatic tumors, hepatic tumors, and biliary tract stones. We obtained MRVE images of the gallbladder, bile duct, and pancreatic duct to assess the clinical usefulness of this method. In the phantom study, a value identical to the actual luminal diameter could be obtained with a threshold of less than 20%. In all clinical cases, we obtained MRVE images of the gallbladder, bile duct, and pancreatic duct using the threshold we had determined appropriate and scored the diagnostic usefulness in each region. The MRVE images of the biliary tract provided much supplementary information, including the presence of stones and of duct invasion by the malignancy as wells as visualization of the post-stenotic portion. MRVE images of the gall bladder did not significantly improve diagnosis (P=0.311), but those of the bile and pancreatic ducts did (P<0.05). In addition, MRVE may aid navigation during cholangioscopy. Thus, MRVE is a clinically useful technique for examining lesions of the biliary tract and pancreas.