Osteoporosis is a common health problem not only in females but also in males, however, studies of osteoporosis in males are relatively rare compared to those in females. This is especially true in genetics studies. We evaluated the effects of PvuII and XbaI polymorphisms in the estrogen receptor alpha (ER-alpha) gene and ApaI polymorphism in the vitamin D receptor (VDR) gene on BMD variation in a random sample of 352 unrelated males from 401 Chinese nuclear families. BMD was measured at the lumbar spine (L1-L4) and hip (femoral neck, trochanter, intertrochanteric region). Raw BMD values were adjusted by age, age(2), height, and weight as covariates. We found no significant results for the 3 individual markers on BMD variation, however, ER-alpha haplotype analyses yielded some interesting results. Carriers of haplotype pX had a 4.98% lower BMD at the trochanter (P = 0.02) and 3.55% lower BMD at the lumbar spine (P = 0.09) than non-carriers. PX subjects had a 3.42% higher BMD at the trochanter and 3.26% higher BMD at the lumbar spine than others (P = 0.07 and P = 0.10, respectively). Such results were highly comparable with the significant or nearly significant interactions between ER-PvuII and ER-XbaI on BMD values at the trochanter (P = 0.03) and spine (P = 0.11). No significant results were observed for the interactions between ER-PvuII and VDR-ApaI, between ER-XbaI and VDR-ApaI, and between any of ER-alpha haplotypes and VDR-ApaI locus. Our results suggest that the ER-alpha haplotypes, not individual markers, may be associated with BMD variation at some skeletal sites in our Chinese male samples.