We examined the potential associations between PvuII and XbaI polymorphisms in the first intron of the estrogen receptor alpha (ER-alpha) gene and bone mineral density (BMD) in a population-based study of 174 postmenopausal Korean women. BMD was measured at the lumbar spine (L2-L4), right femoral neck, right trochanter, and right Ward's triangle. ER-alpha gene polymorphisms were detected by PvuII and XbaI restriction endonuclease digestion of polymerase chain reaction products. Differences in BMD values between the ER-alpha genotypes were analyzed in a general linear model, with adjustments for age, height, weight, and smoking status. The following genotype frequencies were noted: PP, 14.9%; Pp, 46.0%; pp, 39.1%; XX, 3.5%; Xx, 29.3%; and xx, 67.2%. Both the femoral neck and Ward's triangle BMD values in women with the Pp genotype were significantly (P < 0.05) higher than those in women with the pp genotype. No significant effect of the XbaI genotype on BMD was found at any site. Carriers of the pX haplotype were more likely to have lower BMD values at the trochanter than noncarriers, after adjustment for potentially confounding factors. Women with the pp genotype had more previous hip or spine fractures than those with other genotypes (P = 0.05). These results suggest that the PvuII polymorphism and the ER-alpha haplotype may be associated with the BMD at several femur sites in postmenopausal Korean women.