Purpose: To investigate the clinical effect of minimally invasive percutaneous nephrolithotomy (MPCNL) using a patented irrigation and clearance system. Patients and Methods: From August 2008 to August 2009, 60 patients with renal stones >= 2.0 cm were randomly assigned to two groups. Group 1 included 30 patients who were treated by MPCNL through a patented 16F sheath with the aid of a patented irrigation and clearance system combined with a high power holmium laser. Group 2 included 30 patients who were treated by a third generation EMS ultrasound/ballistic trajectory lithotripsy and clearance system through a standard 24F sheath. The differences in (1) average time needed for stone clearance; (2) percentage of cases in which one surgery resulted in freedom from stones; (3) mean renal pelvic pressure; and (4) mean amount of intraoperative bleeding were compared. Results: Compared with the EMS ballistic trajectory/ultrasound lithotripsy and clearance system, the MPCNL irrigation and clearance system had a significantly higher percentage of stone-free outcomes after one surgery and a lower amount of introperative bleeding (P < 0.05). There was no difference in mean stone-clearance time and mean renal pelvic pressure (P > 0.05). When comparing the cases with one percutaneous tract in the patented system group with the cases with one percutaneous tract in the EMS system group, the findings were similar. Conclusion: The patented MPCNL irrigation and clearance system is safe and highly efficient in managing renal stones.