In the present study, we examined the genotypes distribution of Pvu II estrogen receptor (ER) gene polymorphism and its association to bone mass in Thai females. Subjects consisted of 134 Thai females 54 of whom were premenopausal and 80 were postmenopausal. Pvu II ER gene polymorphism was determined by PCR-RFLP. Capital P represents the absence of the restriction site while small p indicates the presence of the restriction site. Forty nine (36.6%) of the subjects had pp genotype, while 59 (44.0%) had Pp genotype and 26 (19.4%) had PP genotype. There was no significant difference in age, body weight, height and calcium intake in premenopausal women with different genotypes. The results including years since menopause were similar in postmenopausal women. When including ER gene genotypes, age, body weight, height and dietary calcium intake in a stepwise multiple regression model, it was found that besides body weight ER gene polymorphism was associated with bone mineral density (BMD) at AP spine (p < 0.05), lateral spine (p < 0.05) femoral neck (p < 0.05) and femoral trochanter (p < 0.05) with the pp genotype having the least BMD. ER gene polymorphism was the only factor associated with BMD at Ward's triangle, (p < 0.05) while only body weight was associated with BMD at distal and mid radius. There was no difference in serum intact osteocalcin (OC) concentrations among subjects with different genotypes. ER gene polymorphism was not related to BMD in postmenopausal women at any skeletal site. Similarly, serum intact OC levels were not different among postmenopausal women with different genotypes. We concluded that Pvu II estrogen receptor gene polymorphism is associated with bone mineral density in premenopausal women but not in postmenopausal women. Estrogen receptor gene polymorphism may have a modulatory role in calcium and bone metabolism during adolescence and young adulthood.