Postmenopausal osteoporosis (PMO) is considered a polygenic disease. The estrogen receptor beta (ESR2) gene is a candidate mediating the genetic influence on bone mass and the risk of osteoporosis. The aim of this study is to investigate the association of a cytosine-adenine (CA) repeat polymorphism in the fifth intron of the ESR2 gene with PMO in Chinese Han population. The CA repeat polymorphism was genotyped in a case-control study, involving 78 femoral neck PMO patients vs. 122 controls and 108 lumbar spine (L2-4) PMO patients vs. 92 controls. The (CA)(n) < 22 and (CA)(n) > or = 22 alleles were designated short (S) and long (L), respectively. ESR2 genotype was categorically defined as SS (2 S alleles), SL (having the mixed S and L alleles), and LL (2 L alleles). At both the femoral neck and the L2-4 region, LL genotype and L allele frequencies of the PMO group were significantly higher than those of the control group (P < 0.01). The subjects with the SL, the LL, and the combined SL and LL genotype had a significant increased risk of PMO when compared with those with the SS genotype (P < 0.05). After adjustments for age, years since menopause, menopausal age, and body mass index, logistic regression analysis showed that the subjects with the combined SL and LL genotype had increased risk of PMO when compared with those with the SS genotype both at the femoral neck (adjusted OR 4.923, 95%CI 1.986-12.203, P=0.001) and the L2-4 (adjusted OR 2.267, 95%CI 1.121-4.598, P=0.023). This extensive association study has identified the ESR2 CA repeat polymorphism to be independently associated with PMO at the femoral neck and the L2-4 in Chinese Han population. The data also suggested that the presence of the L allele may dominantly increase the risk of PMO at the two regions.