Background and Purpose: A prospective randomized study was performed comparing miniperc and shockwave lithotripsy (SWL) for treatment of radiopaque 1 to 2cm lower caliceal renal calculi in children to evaluate safety and efficacy of these procedures. Patients and Methods: Pediatric patients (<15 years) with a single radiopaque lower caliceal renal stone 1 to 2cm undergoing treatment between March 2012 and September 2013 in our department were randomized into two groupsgroup A, miniperc; group B, SWL. The two groups were compared statistically regarding patient demographic profile, 3-month stone-free rate (SFR), re-treatment rates, auxiliary procedures, and complications. Results: There were 106 patients enrolled in each group. The mean age (10.3 years vs 10.7 years, P=0.57) and stone size (12.7mm vs 12.9mm, P=0.31) were similar between group A and B patients. The re-treatment rate and auxiliary procedure rate were significantly greater in group B compared with group A (41.5% vs 2.8% and 14.2% vs 5.6%, respectively; P<0.001). The overall 3-month SFR was 94.3% for group A vs 83% for group B (P=0.03). The complication rate (20.7% vs 3.7%; P=0.01) and hospital stay (3.7 days vs 7.1 hours; P=0.01) was significantly higher in group A compared with group B. Blood transfusion was given in 10.3% patients in group A vs none in group B (P=0.01). Conclusions: Miniperc is more efficacious than SWL for treatment of radiopaque lower caliceal renal calculi 1 to 2cm in children in terms of higher SFR and lesser auxiliary and re-treatment rates. Miniperc, however, resulted in more complication, operative time, radiation exposure, and hospital stay.