The objective of this study was to report our pathological findings in nephrectomy specimens from patients treated for non-functioning hydronephrotic kidney due to renal pelvic stone disease. A total of 97 patients who underwent nephrectomy for non-functioning hydronephrotic kidneys between January, 2011 and June, 2014 were retrospectively reviewed. A non-functioning kidney was defined as one having paper-thin parenchyma on urinary ultrasound or computed tomography, exhibiting no contrast visualization in the collecting duct system on intravenous urography and having a split renal function of <10% on nuclear renal function studies. Following pathological evaluation, 9 patients were diagnosed with xanthogranulomatous pyelonephritis, 9 with malignant tumors and 79 with chronic pyelonephritis. Of the patients with chronic pyelonephritis, 2 also had renal adenomas. The malignant tumors included 3 transitional cell carcinomas (TCC), 2 squamous cell carcinomas (SCC), 3 renal cell carcinomas (RCC) (1 sarcomatoid, 1 papillary and 1 clear cell RCC), whereas 1 patient had concurrent RCC and TCC. In conclusion, non-functioning kidneys, particularly those with kidney stones, should be managed as possible malignancies, due to the higher incidence of malignant tumors in such patients compared with the normal population.