Background Peroxisome proliferator-activated receptor gamma(PPAR gamma) is involved mainly in adipocyte differentiation and has been suggested to play all important role in the pathogenesis of insulin resistance (IR) and atherosclerosis. The frequencies of 2 common polymorphisins of the PPAR gamma gene, Pro 12Ala single nucleotide polymorphism (SNP) in exon B and C 161 T SNP in exon 6, were investigated in 792 subjects and the correlations between the different genotypes, IR and metabolic syndrome (MS) were analyzed. Methods and Results Anthropometric measurements, fasting glucose, insulin and lipid profiles were measured in 792 people of the Han population in Beijing, China. Homeostatic model assessments and quantitative insulin sensitivity check indices were calculated. MS was diagnosed according to the IDF guidelines (2005) for a Chinese population. Polymerase chain reaction-restriction fragment length polymorphism were performed for DNA genotyping. For the C 161T polymorphism, allele frequencies were 0.804 for the C allele and 0.196 for the T allele. For Pro12Ala, allele frequencies were 0.947 for proline and 0.053 for alanine. There was no Ala12Ala homozygote in the population. No differences were seen in the mean values of age, body mass index (BMI), blood pressure or fasting blood glucose level among different genotypes when analyzed as a whole. Subjects with all A or T allele had lower fasting insulin levels, HOMA-IR levels, and a lower level QUICKI trend. Further analysis by age was conducted, and A or T allele carriers in the <60 year group showed a trend of lower triglyceride and a higher high-density lipoprotein-cholesterol level, but this was not statistically significant. When Subjects were divided into 4 groups according to the combination of genetic alleles of the 2 polymorphisms, the subjects with Pro 12Ala and a T allele simultaneously showed a significantly higher BMI than those without the Ala allele. The presence of a T allele in the C161T polymorphism and Pro12Ala polymorphism seems to affect body weight, which is similar to the results found in previous studies. Conclusions Both polymorphisms showed a significant association with IR, but failed to show an association with MS components. Those with all A allele of Pro 12Ala and a T allele of the C161T polymorphism showed a higher BMI, which requires further investigation.