Introduction: The association between body composition and the hormones has been explored in a limited number of studies. Hence, this study was performed to examine the association between body composition and serum level of leptin among children.  Materials and Methods: This cross-sectional study was conducted among 111 students aged 6-10 years, who were selected from 20 elementary schools in Tehran. We measured fasting plasma leptin by radioimmunoassay. The bioelectrical impedance was used to determine the subjects' body fat mass (FM), fat free mass (FFM) and their distribution in the body. The subjects' physical activity and sleep were recorded for a week by an accelerometer (Actigraph). Results: Results of this study showed no significant difference between boys and the girls regarding the level of leptin, FMI (Fat Mass Index, calculated using FM divided by height squared) and FFMI (Fat Free Mass Index, calculated using FFM divided by stature squared) (P>0.05). FMI and FFMI in girls were not significantly associated with leptin whereas in boys, leptin was significantly associated with FMI (&beta=-0.32, P=0.0001) and FFMI (&beta=-0.28, P=0.01) after adjusting for age, physical activity, sleep, dietary intake, and watching TV and computer games. Conclusion: Leptin may influence the gender-related differences of body composition during childhood in boys. Further studies are needed to confirm our findings.