Osteoporosis is a complex disease with a strong genetic component, but the genes involved are poorly defined. To determine whether estrogen receptor beta (ESR2) gene is an osteoporosis risk gene, we examined its association with bone mineral density (BMD) and fracture risk. Using a gene-based approach, a set of 12 polymorphisms of ESR2 was studied in 752 case-control pairs of southern Chinese in ethnicity. Among all polymorphisms, the most significant relation with BMD and fracture risk was observed with T-1213C. Subjects with low BMD had a higher frequency of the variant C allele of T-1213C (cases 11.4%, control 8.4%, P = 0.02). The C allele was associated with 4% reduction in BMD at both the spine and hip in women, and 11% reduction in spine BMD and 9% reduction in hip BMD in men. Similar results were seen with SNP haplotype analysis. Subjects with the C allele of T-1213C were associated with higher risks of osteoporosis and BMD T scores < or = -2.5 (odds ratios: 2.2 at spine and 3.5 at femoral neck for women; 3.5 at lumbar spine for men). Postmenopausal women carrying this C allele were associated with 2.22-fold increased risk of osteoporotic fractures (95% confidence interval 1.26-4.25) even after adjusting for BMD. In conclusion, ESR2 is involved in BMD determination in both sexes. The T-1213C polymorphism influences the risk of fracture in postmenopausal women independent of BMD.