Aim To investigated the polymorphisms of the apolipoprotein AI(apoAI) gene with coronary heart disease (CHD) and atherosclerotic cerebral infarction (ACI) patients in Beijing area. And to evaluate the association of polymorphisms of MspI with variable of lipid. Methods Using the polymerase chain reaction (PCR), We studied the polymorphism of MspI in 226 patients with CHD and 236 patients with ACI and 321 age-matched healthy individuals. Results The polymorphic site was the MspI site in the third intron of apoAI gene, whose presence has previously been shown to be associated with CHD. The frequencies of the MspI minor allele M 2 were 0.387 in CHD patients (P<0.05). There were no difference in the frequencies of minor allele M 2 between ACI patients and controls (P>0.05). There were apparent differences in the genotypes of apoAI gene and several lipid variables among the CHD patients, ACI patients and control group. Conclusions M 2 allele in the third intron of the apoAI gene may associated with CHD and ACI and presumably through its influences on lipid metabolism to increase the susceptibility to atherosclerosis disease.