To investigate the relationship among the PvuII and XbaI polymorphism of estrogen receptor (ER) gene and bone mineral density (BMD, z-score) and bone biochemical markers in Chinese postmenopausal women.The BMD of lumbar vertebrae (L2-4) and femoral neck (FN) of 186 postmenopausal women (aged 65.0 +/- 0.6 yr) were measured by DEXA. The polymorphism of ER gene (PvuII and XbaI) was detected by PCR-RFLP method. Serum AKP, BGP and urinary Pyd were measured by ELISA. Results The polymorphism of ER receptor can be divided into two sets: PP (14.5%), Pp (50.0%), and pp (35.5%); and 3 PvulI RFLPs and XX (7.0% ), Xx (27.4%), and xx (65.6%) 3 XbaI RFLPs. The bone markers were not significantly different among the 3 groups in each of the two sets of polymorphism. The FN BMD of women of pp genotype was higher than that of Pp genotype (P = 0.02). The BMD of 12-4 was higher in women of XX genotype than those in women of Xx and xx genotypes (P = 0.0003 and 0.0002 respectively). Women without Px haplotype (PPXX, PpXX, ppxx, n=79) had higher L2-4 BMD (P = 0.02) and FN BMD (P = 0.03) and lower serum AKP (P = 0.04) than those with Px genotype (PPxx and PPXx, Ppxx, PpXx, n=107).pp and XX genotype of ER gene may play a certain role in maintaining FN and L2-4 BMD. The genotypes without Px haplotype might exert some favorable effect on BMD, while those with Px haplotype may be harmful to bone