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Objective:To investigate the relationship between the rs9729,rs11574129,BsmI (rs1544410),TaqI (rs731236) and DdeI (rs3782905) polymorphisms of the vitamin D receptor (VDR) gene and kidney stone formation in a study group from Guangxi.Methods:A hospital based casecontrol study including 890 patients with kidney stone formation and 822 age and sex-matched controls without stone formation was conducted.Five single-nucleotide polymorphisms (SNPs) of the VDR gene were studied using SNPscanTMhigh-throughput SNP classification assays.Results:The T allele variant of rs9729 significantly increased the risk of kidney stone formation (P =0.021).In particular,a significantly increased risk of kidney stone formation was found in the combined genotypes TG/TT of rs9729 compared with the wild GG genotype after covariate adjustment.However,after gender stratification analysis,compared with the wild GG genotype,the GT,TT and GT/TT genotypes of rs9729 increased the risk of kidney stone formation in males.Moreover,the GA and GA/GG genotypes of rs11574129 were associated with increased risk of kidney stone formation in males.By contrast,the GC and GC/CC genotypes of DdeI (rs3782905) significantly decreased the risk of kidney stone formation in males.Haplotype analysis suggested that the five-locus poly morphism of VDR was significantly related to kidney stone formation in male participants (P =0.0025).Conclusion:The T allele variant of the rs9729 polymorphism of the VDR gene was significantly related to the risk of kidney stone formation.Gender may affect the association between the rs9729,rs11574129 and DdeI polymorphisms of the VDR gene and the risk of kidney stone formation in the Chinese population.