Abstract: Objective To investigate the association of peroxisome proliferator activated receptor(PPAR)γ2 gene Pro12Ala and C1431T polymorphisms with metabolic syndrome.Methods Matrix assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF-MS) was used to detect PPARγ2 gene Pro12Ala and C1431T genotypes in 489 subjects(245 metabolic syndrome patients and 244 controls).Results The frequencies of Pro12Ala genotype(χ²=0.050,P=0.822) and allele(χ²=0.108,P=0.742) showed no significant differences between the patients and the controls.The frequencies of C1431T CC genotype and C allele for metabolic syndrome patients were all higher than those of the controls(CC genotype:78.8%vs 68.4%,P=0.01; C allele:87.6%vs 83.0%,P=0.044).Multiple logistic regression analyses suggested that risk factor for metabolic syndrome was CC genotype(OR=2.043).The results of interaction analyses for different factors indicated that the risk for metabolic syndrome in alcohol drinkers with CC genotype was 2.788 times of that non-drinkers with CT/TT genotype.Conclusion The PPARγ2 gene C1431T polymorphism is associated with metabolic syndrome risk in Kazakh.CC genotype and C allele may serve as genetic risk factors of metabolic syndrome and CC genotype and alcohol drinking may have additive effect on metabolic syndrome.