Aim To evaluate the effect of apolipoprotein E (apo E) polymorphism on serum lipids and the relationship between apo E polymorphism and coronary stenosis. Methods The polymorphis site of apo E gene were studied using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 95 cases with coronary artery disease (CAD) and in 46 controls of equivalent age. The serum lipids and apolipoprotein B (apo B) levels were measured in the two groups. Results The frequencres of apo E3/4 genotype and apo E4 allele were significantly higher in 55 cases of CAD with multiple vessel dissease (MVD) and in 40 cases of CAD with single vessel disease (SVD) than in 46 controls (P<0.01), while there were significantly higher in the MVD groups than in the SVD groups (P<0.05). Apo E3/4 genotype had significantly higher serum total cholesterol (TC), LDL-cholesterol (LDLC) and apo B levels and lower HDL-cholesterol (HDLC) level compared to apo E3/3 and apo E₂/3 genotypes in the patients and in the controls. In the patients , apo E3/4 genotype had significantly higher TC, LDLC and apo B levels and lower HDLC levels compared with in the controls . Conclusions It is concluded that apoE polymorphism is involved in cholesterol metabolism , where apo E4 allele is associated with an increased risk of CAD. In CAD cases , an increased frequency of apo E4 allele is associated with an increased severity of coronary stenosis. Therefore it is assumed that there is certain relation between apoE4 allale and severity of coronary stenosis.