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OBJECTIVE This study aimed to evaluate the efficacy of our counter-irrigation technique versus the standard technique in percutaneous nephrolithotomy (PCNL) by assessment of the stone-free rate after the procedures and its safety in terms of comparing the intraoperative time, Hb deficit, blood transfusion, length of hospital stay, auxiliary procedures, and perioperative complications with that of the standard one. METHODS This prospective randomized trial was conducted on patients with renal stone 2-3 cm in diameter without contraindications to PCNL. The patients were randomized into group A in which the counter-irrigation technique has been performed and group B who were managed by the standard technique. The preoperative characteristics including demographic data and stone parameters were compared between both groups. The primary outcome was the stone-free rate assessed by noncontrast spiral CT after 3 months. The secondary outcome included intraoperative time, Hb deficit, blood transfusion, hospital stay, auxiliary procedure required, and rate of complications. RESULTS Forty-eight patients were included in this study. Overall, no significant difference was observed between both groups regarding preoperative characteristics, Hb deficit, and complication rate. Operative time was significantly shorter in group B (p = 0.001). None of our patients required blood transfusion. The stone-free rates at 3 months were significantly better in group A (95% for group A and 70% for group B, p = 0.04). CONCLUSIONS Our results indicate that our counter-irrigation technique has lower stone migration with subsequent significantly better stone-free rate versus the standard technique. We can recommend this technique as a potentially valid option for cases with large stone burden when the access to the upper calyx is feasible to minimize significant residual fragments.