<b><i>Background:</i></b> Bone mass acquisition in childhood is directly linked to adult bone mineral density (BMD) and fracture risk. BMD is a heritable trait, more than 70% of its variability among a population is affected by genetic factors. <b><i>Objectives:</i></b> In the present study, we wanted to investigate the association between estrogen receptor alpha (ESR1) polymorphisms, <i>PvuII</i> (rs2234693) and <i>XbaI</i> (rs9340799), and bone area, bone mineral content (BMC), and BMD of the lumbar spine, femoral neck, and also of the total body less the head in Iranian children. <b><i>Methods:</i></b> The ESR1 gene <i>PvuII</i> and <i>XbaI</i> genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism. Bone area, BMC, BMD, and bone mineral apparent density (BMAD) were assessed by dual-energy X-ray absorptiometry (DEXA). Linear regression was carried out to examine the effects of the ESR1 (<i>PvuII</i> and <i>XbaI</i>) polymorphisms on DEXA outputs when adjusted for confounding factors (i.e., age, sex, BMI, and pubertal stage) in 3 models. <b><i>Results:</i></b> ESR1 (<i>PvuII</i>) gene polymorphisms (CT vs. CC) showed significant effects on the BMC of the total body less the head in all 3 models. For ESR1 (<i>XbaI</i>), individuals with the AG genotype had higher lumbar spine BMD and lumbar spine BMAD compared to other genotypes. <b><i>Conclusions:</i></b> It seems that the <i>PvuII</i> and <i>XbaI</i> polymorphisms of ESR1 could be associated with BMC and BMD variation in Iranian children and adolescents.