Background Some 60-80% of the variability in bone mineral density (BMD) is determined by genetic factors. In the present study, we investigated the impact of the rs2302685 polymorphism of LRP6 on BMD and body composition in Iranian children. Methods In total, 200 children (101 boys and 99 girls) were enrolled in the study. Body composition and BMD were computed using the Hologic DXA System (Hologic, Marlborough, MA, USA). The single nucleotide polymorphism of LRP6 rs2302685 (V1062I) was determined using a polymerase chain reaction/restriction fragment length polymorphism. A generalized linear model was performed to find the association between LRP6 polymorphisms, BMD and body composition in two adjusted models. Results In model 1, a significant difference was found between LRP6 (rs2302685) polymorphism, trochanteric BMD (p= 0.007), intertrochanteric BMD (p= 0.007), total fat (p= 0.001), total fat (%) (p= 0.034), total lean mass (p= 0.031), total Lean + BMC (p= 0.036) and total mass (p= 0.001). In model 2, LRP6 (rs2302685) polymorphisms showed a significant effect on the trochanteric BMD (p= 0.005), intertrochanteric BMD (p= 0.005), total fat (p= 0.001), total fat (%) (p= 0.013) and total mass (p= 0.01). Total fat, total fat (%) and total body mass were higher in subjects with the CC genotype compared to the TT/CT genotype, whereas total lean mass and total Lean + BMC were higher in the TT/CT genotype. Conclusions The present study shows that the LRP6 polymorphism may be associated with body composition and BMD in Iranian children.