Objectives Peroxisome proliferator-activated receptor-γ2(PPARγ2) variant Pro12Ala was demonstrated with risk of coronary heart disease (CHD) and type 2 diabetes mellitus (T2DM). Another variant C-689T in the promoter was reported with lower receptor activity but lack of reports on association between C-689T and CHD or T2DM. Methods A total of 351 subjects without CHD and T2DM (controls) and 125 patients with CHD and T2DM (cases) were enrolled in our case-control study. Polymerase chain reaction-restricted fragments length polymorphism (PCR-RFLP) was used to detect Pro12Ala and C-689T polymorphisms. And effects on CHD merged with T2DM of the two polymorphisms were analyzed in individual and haplotype analyses. Results In the study, Pro12Pro, Pro12Ala and Ala12Ala genotype frequencies were 92.9%, 6.8% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively whilst CC, CT and TT genotype frequencies were 93.4%, 6.3% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases respectively. Pro12Ala and C-689T polymorphisms were in strong linkage disequilibrium (D’=0.81, P=0.000) and the observed haplotype frequency of Pro-C, Pro-T, Ala-C and Ala-T was 0.957, 0.006, 0.008 and 0.028 respectively. No significant associations were detected between the two polymorphisms and CHD merged with T2DM in either individual or haplotype analyses. In subjects with obesity [body mass index (BMI)≥25 kg/m2], we found that both Pro12Ala and C-689T polymorphisms were associated with BMI. In haplotype analyses, we found that Pro12Ala and C-689T haplotypes had associations with systolic blood pressure in total population, with BMI, waist circle and total cholesterol(TC) in obesity subgroup and with fasting blood glucose and TC in males. Conclusions PPARγ2 Pro12Ala and C-689T polymorphisms and haplotypes affect the profiles of CHD merged with T2DM in Chinese Han people. Objectives Peroxisome proliferator-activated receptor-γ2 (PPARγ2) variant Pro12Ala was demonstrated with risk of coronary heart disease (CHD) and type 2 diabetes mellitus (T2DM). Another variant C-689T in the promoter was reported with lower receptor activity but lack of Reports on association between C-689T and CHD or T2DM. Methods A total of 351 subjects without CHD and T2DM (controls) and 125 patients with CHD and T2DM (cases) were enrolled in our case-control study. Polymerase chain reaction-restricted fragments And effects on CHD merged with T2DM of the two polymorphisms were analyzed in individual and haplotype analyzes. Results In the study, Pro12Pro, Pro12Ala and Ala12Ala genotype frequencies were 92.8%, 7.2% and 0.0% in cases respectively whilst CC, CT and TT genotypes were 93.4%, 6.3% and 0.3% in controls; 92.8%, 7.2% and 0.0% in cases eachl Pro12Ala and C-689T polymorphisms were in strong linkage disequilibrium (D ’= 0.81, P = 0.000) and the observed haplotype frequency of Pro-C, Pro-T, Ala-C and Ala-T was 0.957, 0.006, 0.008 and 0.028 respectively. No significant associations were detected between the two polymorphisms and CHD merged with T2DM in both individual or haplotype analyzes. In subjects with obesity [body mass index (BMI) ≥25 kg / m2], we found that both Pro12Ala and C -689T polymorphisms were associated with BMI. In haplotype analyzes, we found that Pro12Ala and C-689T haplotypes had associations with systolic blood pressure in total population, with BMI, waist circle and total cholesterol (TC) in obesity subgroup and with fasting blood glucose and TC in males. Conclusions PPARγ2 Pro12Ala and C-689T polymorphisms and haplotypes affect the profiles of CHD merged with T2DM in Chinese Han people.