Bone mineral density (BMD) is used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. Osteoporosis, characterized mainly by decreased BMD, is a highly heritable complex disorder and a major public health concern to hundreds of millions of elderly persons worldwide. However, the specific genetic variants determining risk for low bone density are still largely unknown. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in ESR1 gene with low bone density. By examining genotype data of a total of 1813 women in the Korean Association REsource (KARE) study, we discovered the ESR1 gene polymorphisms are associated with decreased BMD and osteoporosis. The results on the BD-RT (bone density estimated by T-score at distal radius), three SNPs (rs2248586, rs9371557, and rs1569788) within the ESR1 gene were significantly associated with bone density. The results on the BD-TT (bone density estimated by T-score at midshaft tibia), five SNPs (rs9371552, rs2248586, rs712221, rs7772475, and rs3798577) were significantly associated with bone density. The SNP rs2248586 within the ESR1 gene had commonly significance in both BD-RT (${eta}$=-0.151, dominant P=0.049) and BD-TT (${eta}$=-0.156, dominant P=0.039). In the SNP rs2248586, their ${eta}$-values in BD-RT and/or BD-TT showed consistent trends with the odds ratios (ORs) of osteoporosis. In summary, we found statistically significant SNPs in ESR1 gene that are associated with both decreased BMD and osteoporosis traits. Therefore, our findings suggest ESR1 gene could be related to pathogenesis of osteoporosis.