Abstract. The present study aimed to compare two-dimensional (2D) and three-dimensional (3D) magnetic resonance cholangiopancreatography (MRCP) for the assessment of pancreatic cystic lesions. Between February 2009 and December 2011, 35 patients that had been diagnosed with pancreatic cystic lesions, which was confirmed by surgery and pathology, underwent pre-operative 2D or 3D MRCP for preoperative evaluation. In the present study, the quality of these 2D and 3D MRCP images, the visualization of the features of the cystic lesions, visualization of the pancreatic main duct and prediction of ductal communication with the cystic lesions were evaluated and compared using statistical software. The 3D MRCP images were determined to be of higher quality compared with the 2D MRCP images. The features of the cystic lesions were visualized better on 3D MRCP compared with 2D MRCP. The same capability for the visualization of the segment of the pancreatic main duct was exhibited by 3D and 2D MRCP. There was no significant difference between the area under the receiver operating characteristic curve values of 2D and 3D MRCP, which assessed the prediction of communication between cystic lesions and the pancreatic main duct. It was concluded that, compared with 2D MRCP, 3D MRCP provides an improved assessment of pancreatic cystic lesions, but does not exhibit an improved capability for the visualization of the pancreatic main duct or for the prediction of communication between cystic lesions and the pancreatic main duct.