Aim The study was designed to examine the relationship between polymorphism at the apolipoproteinlipoprotein E gene and the risk of coronary artery disease (CAD). Furthermore, the association of the polymorphism with the classical risk factors was analyzed. Methods A total of 124 patients with angiographically verified CAD or myocardial infarction were prospectively evaluated. Data referring to hypertension, diabetes and tobacco consumption were recorded. The plasma levels of total cholesterol, HDL cholesterol, apolipoproteinlipoprotein AI and B and triglycerides were determined. DNA was obtained from the 124 patients and from 70 controls. In order to determine the apolipoproteinlipoprotein E genotypes, DNA was PCR amplified and digested with HhaI. Results The frequency of the ε2, ε3 and ε4 are 0.155±0.300, 0.648±0.342, and 0.197±0.246 in Uygur population and 0.081±0.196, 0.772±0.315, and 0.146±0.237 in Han population respectively. The frequency of the ε2, ε3 and ε4 are 0.060±0.198, 0.758±0.302, and 0.182±0.250 in the patient group and 0.193±0.286, 0.671±0.370, and 0.136±0.224 in the control group respectively. ε2 frequency of Uygur' patient and control are 0.050±0.221 and 0.290±0.336. Serum LDL cholesterol, TC and TG values tended to decrease from the apolipoproteinlipoprotein E-4 phenotypes to apolipoprotein E-2 phenotypes. Deletion polymorphism of ε2 compared with common risk factors for CAD, its risk ratio (RR) is 4.38. Conclusion These studies showed that the apolipoprotein E phenotype distribution in Uygur population differed significantly from Han population in Xinjiang. CAD patients have significantly lower ε2 allele than controls especially in Uygur population. Deletion of ε2 may be a risk factor for CAD.