To investigate the relationships between the polymorphisms of estrogen receptor (ER) gene, bone mineral density (BMD) and bone biochemical markers in Chinese postmenopausal women.BMD of lumbar spine and femoral neck were measured using dual-energy X-ray absorptiometry (DEXA) in 186 Chinese postmenopausal women. The PvuII and XbaI polymorphisms of the ER gene were detected using polymerase chain reaction (PCR). Bone biochemical markers, serum alkaline phosphatase, osteocalcin and pyridinoline were measured by ELISA.The femoral neck (FN) BMD (Z score) was higher in pp compared to Pp (-0.01 +/- 0.12 vs. -0.35 +/- 0.09, P < 0.05) while lumbar spine BMD (Z score) was higher in XX type compared to Xx and xx genotypes (0.01 +/- 0.45 vs -1.53 +/- 0.17, -1.29 +/- 0.10, < 0.001 and 0.001, respectively). Women without Px haplotype (n = 79) had a higher BMD Z-score for the lumbar spine (-1.03 +/- 0.14 vs -1.45 +/- 0.11, P < 0.05) and femoral neck (-0.01 +/- 0.11 vs -0.31 +/- 0.09, P < 0.05) than those who had it (n = 107).The present study suggested that the pp and XX genotypes of ER gene might play a certain role in maintaining FN and lumbar spine BMD. ER genotypes without Px haplotype might be favorable to bone mass, while those with it might exert some harmful effect on bone mineral density.