This study aimed to prospectively evaluate the feasibility of three-dimensional (3D), compressed sensing (CS) magnetic resonance urography (MRU), with and without breath-holding (BH), for shortening the acquisition time, with better image quality and diagnostic performance. Forty-five patients were enrolled. BH-CS MRU, navigator-triggered (NT) CS MRU, and conventional NT MRU were performed. Comparisons of acquisition time, image quality (sharpness of urinary tract and background suppression), and diagnostic performance were made among these three protocols. BH-CS MRU was superior to the other MRU protocols, with the shortest acquisition time and better image quality with comparable diagnostic performance.