Aim To investigate the relationship between apolipoprotein E (apo E) genotype and acute myocardial infarction(AMI) and the influence of apolipoprotein E phenotype on serum cholesterol metabolism. Methods Polymorphism of apolipoprotein E gene were detected by polymerase chain reaction fragmant length polymorphism (PCR RFLP) in a cross sectional study of 50 patients with AMI and 100 healthy subjects. The lipids of these subjects were measured with enzyme’s methods. Results Comparied with control group, the distribution of apolipoprotein E ε4 allele’s and genotype’s frequencies in AMI group were increased(P<0.05), patients with ε4 carrier had higher total cholesterol. Low density lipoprotein(LDL) cholesterol and apolipoprotein B concentrations than subjects with homozygous for ε3(P<0.05). Conclusion Apolipoprotein E polymorphism is associated with AMI and affects the metabolism of serum cholesterol.