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The objective of this study was to audit the costs of retrograde intrarenal surgery (RIRS) and micropercutaneous nephrolithotomy (microperc) and compare them in terms of cost-effectiveness. We performed a retrospective analysis of 63 patients who underwent microperc and 48 patients who underwent RIRS. The cases, performed between first use and first repair, were used for this initial study. The costs associated with performing RIRS and microperc, including the costs of devices, disposables, hospitalization, and additional required treatments, were audited. The main perioperative and postoperative parameters were collected, including operation time, JJ stent requirements, used disposables, stone-free rates, and complications. Statistical analyses of the means of continuous variables were performed using Student's t test and the Mann-Whitney U test. Categorical variables were analyzed using Chi-squared tests. The mean cost of RIRS was $917.13 ± 73.62 and the mean cost of microperc was $831.58 ± 79.51; this difference was statistically significant (p < 0.001). The mean operation time of the RIRS group was significantly shorter than the microperc group (55.62 ± 19.62 min and 98.50 ± 29.64 min, respectively, p < 0.001). The assessment of required additional treatment showed that it was significantly higher in the RIRS group than the microperc group (p = 0.02). The stone-free rate for RIRS was 66.6 and 80.9 % for microperc; this difference was not statistically significant (p = 0.12). In our series, the use of microperc is less expensive than RIRS due to additional required treatments and ancillary equipment in RIRS. RIRS is more effective than microperc in terms of operation time and more effective use of operation rooms.