Aim: Percutaneous nephrolithotomy (PNL) and retrograde intrarenal surgery (RIRS) are common surgical methods in the treatment of kidney stones. Possible effects on kidneys are an important factor in determining the surgical procedure and the surgical method. In our study, kidney injury molecule-1 (KIM-1) and myo-inositol oxygenase (MIOX) were used to compare acute kidney injury in patients that underwent PNL and RIRS. Material and Method:Eighty patients aged 20 to 75, who underwent PNL or RIRS in our urology clinic between November 2018 and February 2020 were included in the study. In this prospective study, the demographic characteristics, stone size, operation time, preoperative and postoperative hemoglobin and biochemistry values of the patients were recorded. 5 cc blood samples taken from the patients before the operation and at the fourth hour after the operation were centrifuged and kept at -80 °C, and the KIM-1 and MIOX levels were measured in the biochemistry department. Results: There was no difference between the groups in terms of demographic data; however,the operation time and length of hospital stay were significantly longer in the PNL group. The mean increase in MIOX was 10.583±9.73 ng/ml and 7.501±16.46 ng/ml in the PNL and RIRS groups, respectively. Although there was a statistically significant increase in both groups, this increase was greater in the PNL group. A significant increase was observed only in the PNL group in the postoperative period (p=0.003). Discussion and Conclusion:The findings of the study suggest that the PNL procedure causes more damage to the kidneys than RIRS.