The purpose of this study is to determine the perioperative risk factors for increased blood loss in children undergoing percutaneous nephrolithotomy (PCNL).We retrospectively reviewed the data on pediatric patients who had undergone PCNL for stone disease in our department. Blood loss estimation was quantified by measuring the changes in hematocrit plus the volume of red blood cells transfused. Univariate and multivariate linear regression analyses were performed to evaluate risk factors associated with increased blood loss after pediatric PCNL. Variables included patient, stone, and treatment parameters. The study group consisted of 105 renal units in 97 children with a median (interquartile range) age of 5 (3-9) years. On univariate linear regression analysis female gender (p = 0.030), absence of hydronephrosis (p = 0.013), increasing stone burden (p = 0.002), staghorn stone type (p = 0.013), multi-tract access (p < 0.001), and prolonged operative time (p < 0.001) were significantly associated with increased blood loss after pediatric PCNL. However, multivariate linear regression analysis demonstrated that the only independent risk factors for increased blood loss following pediatric PCNL were degree of hydronephrosis (B -1.329, 95% CI -2.451 to -0.208, p = 0.021), number of tracts (B 2.545, 95% CI 0.221-4.869, p = 0.032), and operative time (B 0.031, 95% CI 0.008-0.053, p = 0.007). Identifying pediatric patients at increased risk of bleeding following PCNL is crucial to minimize morbidity and hospital stay, and thus, the cost of treatment. Our study demonstrated that degree of hydronephrosis, number of tracts and operative time are important factors in reducing blood loss during pediatric PCNL.