The aim of this study is to compare the effectiveness and the relative risk of postoperative fever between percutaneous nephrolithotomy and retrograde intrarenal surgery for the treatment of renal stones. At the Cannizzaro Hospital in Catania, a total 168 patients with one or more renal stones underwent one of more interventions, resulting in 177 independent records; 62 records related to PCNL treatment and 115 records involved RIRS treatment. To assess the relationship between patient and stone characteristics on the one hand and stone-free rate and the incidence rate of postoperative fever on the other, a generalized additive logistic models was used. We found that stone burden, defined in terms of stone diameter, the number of stones and stone density, is a significant predictor for the success of the intervention. Furthermore, PCNL treatment was significantly less successful for stone in the middle calyx, whereas RIRS obtained significantly lower success rate for stone in the lower calyx that had a sharp infundibular angle. Importantly, for renal stones with a diameter up to 2 cm, RIRS has a very similar success rate compared to PCNL. Stones with a diameter larger than 2 cm are best treated by PCNL. Across the two treatments, older patients and men have lower incidence rate of postoperative fevers. The fact that RIRS has much lower postoperative fever rates for male and younger patients compared to PCNL, means that RIRS could be the treatment of choice for small and midsized stones for such patients.