Background <p>Obesity in children is a serious health issue. In this study, we investigated the association of ESR1 rs2234693 (<i>PvuII</i>) and rs9340799 (<i>XbaI</i>) with obesity-related phenotypes and body composition in Iranian children and adolescents. 272 healthy children and adolescents aged between 9 and 18 years were randomly selected and registered for genotyping. rs2234693 (<i>PvuII</i>) and rs9340799 (<i>XbaI</i>) single nucleotide polymorphism were identified using restriction fragment length polymorphism. A One-way ANOVA with Tukey post hoc analysis was conducted to examine the effects of rs2234693 (<i>PvuII</i>) and rs9340799 (<i>XbaI</i>) on body composition variation across three genetic models. Linear regression analysis was employed to test the association between the rs2234693 (<i>PvuII</i>) and rs9340799 (<i>XbaI</i>) genotypes and body composition, while controlling for confounding factors such as age, sex, and puberty.</p> Results <p>The <i>PvuII</i> (rs2234693) polymorphism was found to be associated with total lean mass, total body mass, total body fat percentage, lean mass index, android lean mass, and appendicular lean mass in both unadjusted co-dominant and dominant models. The individuals with <i>PvuII</i> (rs2234693) C allele showed higher values of android lean mass and ALM compared to non-carriers.</p> Conclusion <p>This study suggests that the C allele of PvuII (rs2234693) may have beneficial effects on the development of lean mass in Iranian children and adolescents.</p>