We aim to compare the outcomes, including the morbidity and success rates in children undergoing percutaneous nephrolithotomy (PCNL) using different sized devices. According to the size of instruments used during surgery, three different groups (ultra-mini-PCNL, mini-PCNL and adult size PCNL) were composed and the outcomes were compared between the groups. PCNL was applied to 225 renal units of 220 children, including 5 patients with bilateral kidney stones. Percutaneous nephrolithotomy was performed using adult instruments (24 F) in 82 renal units, using pediatric instruments (18 F) in 89 and using minimal-size instruments (9.5 F) in 50. One-hundred and twenty-four girls and 96 boys with a mean age of 8.33 (< 17) years were assessed. Stone-free rates were 78 % in group 1 (n = 39) using 9.5 F nephroscope, 75.8 % in group 2 (n = 69) using 18 F nephroscope and 71.4 % in group 3 (n = 60) using 24 F nephroscope. Time to access the collecting system, operative time, duration of nephrostomy and average postoperative hospital stay did not differ between the groups. However, mean hematocrit drop and stone burden were significantly lesser in ultra-mini-PCNL group. There was no significant difference in the complication rates between the groups, according to the modified Clavien classification system. As the important complication of PCNL, bleeding seems to be associated with diameter of dilatation, calibre of nephroscopes and stone burden. To reduce the certain complications, pediatric type of instruments is suitable but the use of adult instruments and techniques may achieve equal results.