Abstract: Objective To investigate the association between lipoprotein lipase gene Hind Ⅲ,S447X polymorphism and metabolic syndrome and its components.Methods PCR-RFLP was used to detect genotypes of lipoprotein lipase Hind Ⅲ and S447X among 401 subjects(201 controls and 200 metabolic syndrome patients).Results The genotype frequencies of H+H-/H-H-,H-allele,SX/XX,and X allele for metabolic syndrome were significantly lower than those of controls(H+H-/H-H-:33.5% vs 46.8%,P=0.012;H-allele:22% vs 28.6%,P=0.031;SX/XX:10.5% vs 22.9%,P=0.001;X allel:5.5% vs 12.44%,P=0.001).The waist circumference(WC),systolic blood pressure(SBP),diastolic blood pressure(DBP),trighyceride(TG),and fasting plasma glucose(FPG) in subjects with H+H-/H-H-genotype were significantly lower than those of with H+H+ genotype,and the high-density lipoprotein-cholesterol(HDL-C) among the subjects with H+H-/H-H-was significantly higher than that of with H+H+ genotype(P0.05 for all).The WC,SBP,DBP,TG and FPG in the subjects with SX/XX genotype were significantly lower than those of with SS genotype,and HDL-C was significantly higher than that of with SS genotype(P0.05 for all).The frequencies of H+H+ and SS genotype were increased along with the growing number of metabolic syndrome component.Conclusion The lipoprotein lipase gene Hind Ⅲ and S447X polymorphism are associated with metabolic syndrome risk in Kazakh,and H+H-/H-H-genotype,H-allele,SX/XX genotype and X allele may serve as protective factors for metabolic syndrome.H+H-/H-H-and SX/XX genotype has beneficial effect for all metabolic syndrome components,and the frequencies of H+H+ and SS genotype increase along with the number of metabolic syndrome component.