We have developed an MR method to measure the volumes of renal cysts and parenchyma in patients with polycystic kidney disease. Phantoms were designed to simulate polycystic kidneys. Four patients were recruited. MR scans were performed on the phantoms and patients. A stereology technique was applied for image segmentation and volume measurement. Volumetric measurement of renal cysts and parenchyma was accurate in phantom studies and reliable in both phantom and patient studies in these limited examples.