Genetic factors influencing acquisition of peak bone mass account for a substantial proportion of the variation in bone mineral density (BMD), although the extent to which genes also contribute to variation in bone loss is debatable. Few prospective studies of related individuals have been carried out to address this issue. To gain insights into the nature of the genetic factors contributing to variation in BMD, we studied 570 women from large Amish families. We evaluated and compared the genetic contributions to BMD in pre- and post-menopausal women, with the rationale that genetic variation in pre-menopausal women is due primarily to genetic determinants of peak bone mass, while genetic variation in post-menopausal women is due to the combined genetic effects of peak bone mass and bone loss. Bone mineral density was measured at one point in time at the hip and spine by dual energy X-ray absorptiometry (DXA). We used variance decomposition procedures to partition variation in BMD into genetic and environmental effects common to both groups and to pre- and post-menopausal women separately. Total variation in BMD was higher in post- compared to pre-menopausal women. Genes accounted for 58-88% of the total variation in BMD in pre-menopausal women compared to 37-54% of the total variation in post-menopausal women. In absolute terms, however, the genetic variance was approximately similar between the two groups because the environmental variance was 3 1/2- to 4-fold larger in the post-menopausal group. The genetic correlation in total hip BMD was 0.81 between pre- and post-menopausal women and differed significantly from one, consistent with the presence of at least some non-overlapping genetic effects in the two groups for BMD at this site. Overall, these analyses suggest that many, but not all, of the genetic factors influencing variation in BMD are common to both pre- and post-menopausal women.