men (aged 20–40 years). However, Ichikawa et al.21 showed evidence of an association between the spine BMD and six SNPs in the ALOX12 gene in both White men (aged 18–61 years) and women (aged 20–50 years). The conflicting results may be due to the differences between the participants, especially their ages, ethnicities or some other confounding issue. This is the first study to investigate the possible influence of ALOX12 SNPs and haplotypes on the BMD variation in a non-Caucasian population. Therefore, our results should be interpreted cautiously, and further studies should be conducted to determine the strength of these associations in various populations. We also examined the relationship between the BMD and the TFM and TLM in young men. Our results showed that both the TFM and the TLM had significant positive associations with the BMD, and the TLM was a stronger predictor of the BMD than the TFM, consistent with previous studies.11,47 However, Cui et al.10 reported that the LM was the only independent factor contributing to the BMD, and the FM was negatively related to the BMD in younger men. In contrast, other independent studies have suggested that the TFM has a stronger effect on the BMD in both pre- and post-menopausal women.48 The influence of body composi- tion on the BMD may be confounded by gender, age, menopausal status and other environmental factors.49 Our study has several strengths. First, we chose all six tagging SNPs of the ALOX12 gene. The extensive LD between SNPs guaranteed that the entire gene had been tested for an association with the BMD and obesity phenotypes. Second, our sample was relatively large, composed of 1215 individuals from 400 nuclear families. Therefore, adequate statistical power was ensured to find the genetic variants of modest effect sizes. Third, we performed the QTDT and 1000-permutation analyses to avoid sample heterogeneity and false-positive results because of multiple tests. Our study has several limitations as well. Our nuclear families contained few sibling pairs, and no linkage was detected in this study. Environmental factors such as dietary fat intake were not considered in this study. In conclusion, we have shown that a genetic variation (rs2073438 and haplotype AGAGG) in ALOX12 is associated with the TFM in young Chinese men, but we failed to observe a significant association between SNPs or haplotypes and the peak BMD at any site. Our findings suggest that ALOX12 is potentially important in the pathogenesis of human obesity. 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