To improve understanding of DWI features of complex renal cysts, and compare diagnostic performance of MRI and CT in discrimination of benign and malignant masses. Images of each lesion were analyzed, including size, thickness of wall, number of septum, enhancement of wall/septum, wall nodule, calcification, and cyst content. CT and MRI image characteristics were compared with pathology or follow-up results. The incidences of high signal intensity on DWI were significantly higher in malignant than in benign masses. MRI showed higher AUC than CT for differentiating benign from malignant masses. MRI could be useful in improving diagnosis of complex renal cysts.