Estrogen is now known to play an important role in bone metabolism in men. Thus, we examined possible relationships between polymorphisms of the estrogen receptor (ER)-α and -β genes, bone mineral density (BMD), and rates of bone loss in an age-stratified random sample of 283 Rochester, Minnesota, men aged 22–90 yr. DNA was analyzed for the XbaI and PvuII ER-α and AluI ER-β polymorphisms. The X/P and x/p alleles of the ER-α gene were in strong linkage disequilibrium. BMD at multiple sites did not differ as a function of either the ER-α or -β genotype. However, the ER-α (but not ER-β) genotypes did modulate the previously described relationships between BMD or rates of bone loss and bioavailable estradiol (E₂) levels in these men. At the femoral neck, BMD was associated with bioavailable E₂ levels in men with the XX (R = 0.66) or PP (R = 0.51) genotypes (P < 0.001 for both) but not in men with the xx (R = 0.15; P = 0.188) or pp (R = 0.12; P = 0.356) genotypes. The interactions between bioavailable E₂ levels and the XbaI and PvuII genotypes were significant at the P < 0.001 and P < 0.009 levels, respectively. Moreover, rates of bone loss at the midradius in men aged 60–90 yr were modestly correlated with serum bioavailable E₂ levels in subjects with the X (R = 0.47) or P (R = 0.42) alleles (P < 0.001 for both) but not in those with the xx (R = 0.15; P = 0.430) or pp (R = 0.21; P = 0.372) genotypes. The overall effect of genotype on midradius rate of bone loss was clearly significant for the XbaI polymorphism (P = 0.009) when bioavailable E₂ levels were low (<40 pmol/liter) but not for the PvuII polymorphism. These data thus indicate that the ER-α genotype may modulate the relationship between BMD or rates of bone loss and estrogen levels in men and that bone mass in men with the X or P alleles may be more susceptible to the consequences of estrogen deficiency (and conversely, benefit most from estrogen sufficiency) than in men with the xx or pp genotypes.