Aim To study the function of apolipoprotein E gene polymorphism on coronary heart disease (CHD) and to evaluate the effect of apolipoprotein E gene polymorphism on plasma lipid levels. Methods By using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP), we determined apolipoprotein E genotype of 220 CHD patients and 180 healthy controls. Other plasma lipid levels are measured by routine way. Results 5 genotypes of apolipoprotein E , E3/3, E3/2, E4/3, E4/2 and E4/4 are detected in our study. There are statistically significant differences in apolipoprotein E4/3 and ε4 frequencies between CHD patients and controls (P<0.01). We also find statistically difference in apolipoprotein E3/3 frequencies between the two groups (P<0.05). CHD patients have significantly higher serum total cholesterol (TC) and low density lipoprotein cholesterol (LDLC) than controls (P<0.01). Among different apolipoprotein E genotypes of CHD patients, there are statistically difference in TC and LDLC levels. Conclusion These results suggest that apolipoprotein E gene polymorphism is involved in the occurrence and the development of CHD and affects plasma lipid levels. apolipoprotein Eε4 might be an important genetic factor of CHD.