The purpose of this study is to verify the applicability of S.T.O.N.E. nephrolithometry in pediatric patients. 103 cases of pediatric patients younger than 4 years old with upper urinary tract calculi treated with mini-percutaneous nephrolithotomy from January 2012 to March 2014 were retrospectively reviewed and evaluated using this scoring system. All procedures were performed under general anesthesia, using a 14-French nephroscope through a 16-French working access. All patients were divided into two groups according to the stages of the operations, Group A for one-stage operation and Group B for two-stage operation. 87 cases were male and 16 cases were female with the mean age of 26.5 months. The total operation time of group A was 45.89±5.43 min, and 54.62±5.58 min of group B (p=0.000). The hospitalization for group A and group B was 6.63±1.34 and 7.23±1.24 days, respectively (p=0.134). The total S.T.O.N.E. score was 5.93±0.67 for Group A, and 7.92±1.04 for Group B (p=0.000). On further dividing each group into low/moderate/high complexity according to the total score, more cases of low/moderate complexity in group A and more cases of moderate/high complexity in group B (χ2=38.096, p=0.000) were reported. Our data suggest that S.T.O.N.E. nephrolithometry is applicable in pediatric upper urinary tract calculi assessment and predictive for the complexity of the operation, hospitalization, and even complications after the operation. Yet modification may be necessary to make this scoring system more distinguishable for pediatric cases.