We reported our experience with percutaneous nephrolithotomy in children and compared the outcomes, including the morbidity and success rates, regarding the instruments of different sizes. One hundred and seventy-three paediatric patients, who underwent percutaneous nephrolithotomy in our clinic between 1999 and 2013, were assessed. According to the size of instruments used during surgery, three different groups were formed and the pre- and postopeartive outcomes were compared between the groups. 76 girls and 97 boys with a mean age of 9.24 (a parts per thousand currency sign17) years were assessed. Stone-free rates were 75.6 % in group 1 (n = 82) using 17 F nephroscope, 79.4 % in group 2 (n = 73) using 24 F nephroscope and 72.2 % in group 3 (n = 18) using 26 F nephroscope. Postoperative fever was seen in four, five and one patient in group 1, 2 and 3, respectively. Urinary infection was seen in one patient in group 1 and four patients in group 2. Mean haematocrit drop and stone burden were significantly lesser in group 1. No significant difference was seen in the duration of nephrostomy and hospitalization between the groups. The success rates obtained in the groups using different instrument types (paediatric or adult) were similar. However, age, weight, height, stone burden and bleeding were significantly lesser in group 1 that used paediatric type of instrument. As the most frequent complication of PNL, bleeding seems to be associated with stone burden, the diameter of dilatation and the calibre of instrument. To decrease the particular complications, paediatric type of instruments are convenient and do not affect the success.