The accretion of peak bone mass is largely under genetic control, and one of the potential candidate genes is the estrogen receptor alpha (ERalpha) gene. The association of ERalpha gene polymorphisms with bone mineral density (BMD) was investigated in a group of 147 healthy caucasian children, adolescents, and young adults (57 boys and 90 girls) in a cross-sectional and longitudinal study. The mean age was 11.3 years (4.3-19.9 years) at baseline and 15.6 years (7.6-25.3 years) at follow-up. Lumbar spine, total body BMD, and body composition were measured by dual energy X-ray absorptiometry and expressed as age- and sex-adjusted standard deviation scores (SDS). We analyzed two restriction fragment length polymorphisms, Pvull and Xbal, and haplotypes thereof. Subjects homozygous for haplotype 1 (px) (33% of the population) had 0.4 SD (standard deviation) lower lumbar spine BMD (P = 0.02) and bone mineral apparent density (BMAD) (P = 0.04) than those heterozygous or noncarriers for haplotype 1 (px) at baseline. Analysis of the follow-up data gave similar results. The association was stronger for the prepubertal than for the postpubertal subjects. Vertebral width SDS, total body BMD SDS, height SDS, body mass index SDS, lean body mass SDS, and percentage fat SDS did not significantly differ between the haplotypes. The age of menarche was not related to any of the haplotypes in girls. The present study shows that Pvull-Xbal ERalpha gene polymorphism is associated with BMD during childhood.