Background Retrograde intrarenal surgery (RIRS) is a known option for the treatment of upper tract calculi with an excellent success. However, the reports of RIRS in prepubertal children are limited. In this study, we evaluated the factors which affected the success rate and the complications of RIRS at renal stone treatment in childhood. Methods We retrospectively reviewed the records of children under 14 years old who underwent RIRS for renal stone disease between January 2009 and December 2012. Patients' age, gender, body mass index (BMI), stone size, stone location, stone number, intraoperative complications, stone free status, postoperative complications were recorded. Results There were 80 ureterorenoscopic procedures performed in 58 renal units of 47 children (23 males and 24 females). The patients' ages ranged from 8 months to 14 years (mean age 4.7 ± 3.4 years). There was a difference in the distribution of symptoms in age groups. UTI was higher in the 1-4 years age group, abdominal pain was seen mostly in children aged 5-14 years. Multiple stones (included staghorn stone) were noted in 60.4% of patients. In 27.6% of patients, ureteral stones were accompanied by renal stones in our series. In the infancy group, cystine and staghorn stones were more frequently seen, mostly bilateral. After a single ureteroscopic procedure for intrarenal stones in children, we achieved stone free status in 50.9% of the ureters (n = 26). After the repeated sessions, the stone clearance rate reached to 85.1%. Conclusion Retrograde intrarenal surgery can be used as a first line therapy to treat renal stones in children. This is especially important if an associated ureteral stone is present that requires treatment; or in patients with cystinuria, which is not favorably treated with ESWL. Complications were seen more frequently in patients with cystine stones. Extravasation was noted more frequently in patients admitted with UTIs. There was a significant relationship between the conversion to open procedures and the age groups, with most procedures occurring in infancy. The parents should be informed about the probability of multiple procedures to achieve stone free status. © 2014 Elsevier Inc.