Apolipoprotein E ( apoE - epsilon 2, epsilon 3, epsilon 4 alleles) plays a role in the regulation of lipid metabolism, with the e4 considered to be a risk factor for coronary artery disease ( CAD). We aimed to evaluate the apoE polymorphisms in Brazilians with CAD and their influence on the lipid profile and other risk factors ( hypertension, diabetes mellitus, smoking). Two hundred individuals were examined: 100 patients with atherosclerosis confirmed by coronary angiography and 100 controls. Blood samples were drawn to determine apoE polymorphisms and lipid profile. As expected, the epsilon 3 allele was prevalent in the CAD ( 0.87) and non- CAD groups ( 0.81; P = 0.099), followed by the e4 allele ( 0.09 and 0.14, respectively; P = 0.158). The epsilon 3/3 ( 76 and 78%) and epsilon 3/4 ( 16 and 23%) were the most common genotypes for patients and controls, respectively. The lipid profile was altered in patients compared to controls ( P < 0.05), independently of the e4 allele. However, in the controls this allele was prevalent in individuals with elevated LDL-cholesterol levels only ( odds ratio = 2.531; 95% CI = 1.028- 6.232). The frequency of risk factors was higher in the CAD group ( P < 0.05), but their association with the lipid profile was not demonstrable in epsilon 4 carriers. In conclusion, the epsilon 4 allele is not associated with CAD or lipid profile in patients with atherosclerosis. However, its frequency in the non- CAD group is associated with increased levels of LDL- cholesterol, suggesting an independent effect of the epsilon 4 allele on lipid profile when the low frequency of other risk factors in this group is taken into account.