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Background Ethnicity is shown to be one of important factors affacting bone mineral density (BMD).The present study was performed to compare the association of six markers for five candidate genes with BMD variation in two populations of different ethnicity, Caucasian and Chinese, and the contribution of genotype and ethnicity to this variation in the populations.Methods The studied restriction fragment length polymorphisms were BsaH Ⅰ of the calcium-sensing receptor gene, SacⅠ of the α2HS-glycoprotein (AHSG) gene, PvuⅡ and XbaⅠ of the oestrogen receptor α gene, ApaⅠ of the vitamin D receptor (VDR) gene and BstBⅠ of the parathyroid hormone gene.The association of these markers with BMD was analysed by one-way and two-way ANOVA with adjustment for covariates.Results Two polymorphisms, AHSG-SacⅠ and VDR-ApaⅠ, showed no association with BMD, while the others were associated with BMD variation at some skeletal sites in either males or females.The polymorphisms indicated clear distinctions between the associations depending on ethnicity, gender and skeletal site.Similar patterns were observed in their contribution to the total population BMD variation.Ethnicity appears to have a larger effect on the total population BMD variation in females than in males.It may account, on the average, for about 2% total population BMD variation at the spine of females and about 1% at the hip of males and females.Conclusion The results of the present study suggest that significant interethnic differentiation at some loci may contribute to the significant interethnic difference in BMD.However, this contribution apparently is not large.