We determined the effectiveness of percutaneous nephrolithotomy in children with cystine stones and present the long-term outcomes. We reviewed the data of 65 renal units in 51 children who underwent percutaneous nephrolithotomy for cystine stones between 2000 and 2012. Of the patients 19 (37%) had undergone ipsilateral renal surgery and 11 (22%) had undergone extracorporeal shock wave lithotripsy. Children were designated as being stone-free or having residual stone (any evidence of persistent stone fragments irrespective of size). Medical treatment with α-mercaptopropionylglycine, potassium citrate or potassium sodium hydrogen citrate was recommended for all patients after stone analysis. Median stone burden was 3.3 cm(2) (range 1 to 13) and median patient age was 6 years (1 to 17). Stone-free status was achieved in 41 renal units (63.1%). Stone-free status was increased to 73.8% with additional endoscopic procedures. The remaining patients with residual stones were followed. Complication rate was 15.4%. A total of 35 children (68.6%) receiving regular medical treatment were followed for a median of 95 months (range 6 to 136). The recurrence rate for children achieving stone-free status was 31.2%, and the regrowth rate for children with residual stones was 29.4%. Percutaneous nephrolithotomy is a safe and effective treatment for children with cystine stones. Our high recurrence and regrowth rates emphasize that our treatment schedule is inadequate to prevent recurrent cystine calculi. Additional investigation is needed to determine the optimal medical therapy for preventing recurrence and regrowth of cystine stones.