BACKGROUND Apolipoprotein (apo) E polymorphism plays a role in the development of coronary disease, but their involvement in carotid atherosclerosis is controversial. The aim of this study was to evaluate the role of apo E polymorphism in the development of subclinical carotid atherosclerosis in patients with coronary disease. METHODS In 226 consecutive patients with coronary disease, apo E genotypes were performed by PCR and restriction analysis. Intima-media thickness (IMT) and the presence of atherosclerotic plaques in carotid arteries were evaluated by two-dimension ultrasonography. RESULTS Apo E allele frequencies were: 3=0.70, 4=0.22 and 2=0.08. The only patient with 2/4 genotype was excluded for the analysis. The patients were divided in three groups according to apo E genotype: E2 (2/2, 2/3), E3 (3/3) and E4 (4/4, 4/3). Patients of E4 group had higher values of low-density-lipoprotein (LDL) cholesterol and apo B than patients of E2 group (P< or =0.01). Carotid IMT mean was not different in E3 (0.81+/-0.21 mm), E4 (0.83+/-0.23 mm) and E2 groups (0.76+/-0.17 mm) (P=0.52). Mean differences of IMT in E3 group were not different from those of E2 or E4 groups after adjusting for age and gender in a first analysis, and for age, gender and LDL cholesterol levels in a second one. The number of plaques in apo E3 group was similar to that in apo E2 or apo E4 groups, after adjusting for the same variables. CONCLUSIONS A relationship between subclinical carotid atherosclerosis and apo E polymorphism is not found in patients with coronary disease.