Laparoscopic nephrectomy has become the gold standard procedure for nonfunctioning or symptomatic benign kidneys due to renal calculi, obstructive, refluxive, and inflammatory nephropathies or renovascular hypertension. We aimed to investigate the effect of renal calculi as a reason of non-functioning on the progress and complication rates of the retroperitoneoscopic nephrectomy (RPN).During a 2-year period, 108 patients with benign renal conditions underwent RPN by single surgeon. Among these patients, total of 27 (Group 1) with a non-functioning kidney due to renal calculi were retrospectively compared with 27 patients (Group 2) with other benign renal conditions. The two groups were matched for age, body mass index, and previous renal surgery. We analyzed operative and post-operative findings and complications. The mean age and the BMI of the groups were similar. The operation time was significantly longer in Group 1 than Group 2 (p = 0.0001). There was no significant difference between the groups with respect to mean hemoglobin drop postoperatively (p = 0.9) and hospitalization time (p = 0.06). The perioperative and postoperative complication rates were higher in Group 1 but not statistically different from Group 2 (p = 0.19, p = 0.29, respectively). RPN for nonfunctioning calculous kidneys is more challenging procedure and is associated with prolonged operation time related to difficult dissection of dense adhesions. It can be safely performed by experienced hands with similar perioperative and postoperative complication rates as well as for other benign conditions of the kidney.