We compared the clinical utility of single-shot echo-planar imaging (SS-EPI) using different breathing schemes, readout-segmented EPI and zoomit EPI in the repeatability of apparent diffusion coefficient (ADC) measurements, cortico-medullary contrast to noise ratio (c-mCNR) and image quality. In this institutional review board-approved prospective study, some common clinically applicable diffusion-weighted imaging (b = 50, 400, 800 s/mm2) of kidney on 3.0 T MRI were performed on 22 volunteers using SS-EPI with breath-hold diffusion-weighted imaging (BH-DWI), free-breathing (FB-DWI), navigator-triggered (NT-DWI) and respiratory-triggered (RT-DWI), readout-segmented DWI (RS-DWI), and Zoomit DWI (Z-DWI). ADC and c-mCNR were measured in 12 anatomic locations (the upper, middle, and lower pole of the renal cortex and medulla), and image quality was assessed on these DWI sequences. A DWI with the optimal clinical utility was decided by systematically assessing the ADC repeatability, c-mCNR and image quality among the DWIs. For ADC measurements, Z-DWI had an excellent intra-observer agreement (intra-class correlation coefficients (ICCs): 0.876–0.944) and good inter-observer agreement (inter-class ICCs: 0.798–0.856) in six DWI sequences. Z-DWI had the highest ADC repeatability in most of the 12 anatomic locations of the kidneys (mean ADC absolute difference: 0.070–0.111 × 10−3 mm2/s, limit of agreement: 0.031–0.056 × 10−3 mm2/s). In all DWIs, Z-DWI yielded a slightly higher c-mCNR than other DWIs in most representative locations (P > 0.05), which was significantly higher than BH-DWI and FB-DWI in the middle pole of both kidneys and the upper pole of the left kidney (P < 0.05). In addition, Z-DWI yielded image quality that was similar to RT-DWI and NT-DWI (P > 0.05) and superior to BH-DWI, FB-DWI and RS-DWI (P < 0.05). Our results suggest that Z-DWI provides the highest ADC reproducibility, better c-mCNR and good image quality on 3.0 T MRI, making it the recommended sequence for clinical DWI of the kidney.