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%and0.3% 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%and0.0% 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 0.957,0.006,0.008and0.028 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-689 T haplotypes had associations with systolic blood pressure in total population,with BMI,waist circle and total holesterol(TC)in obesity subgroup and with fasting blood glucose and TC in males.Conclusions PPARγ2Pro12Ala and C-689T polymorphisms and haplotypes affect the profiles of CHD merged with T2DM in Chinese Han people.