Genetic and environmental factors regulate lipid metabolism and phenotypic expression of CAD. In this study we assessed the effects of apoE gene polymorphism and apoA1 gene promoter polymorphism on lipid metabolism and risk for CAD. In a case-control study, 166 patients with CAD were compared with 130 healthy subjects. The apoE allele frequencies of patients vs. control group were 6.3% vs. 7.7% for e2, 84.3% vs. 84.6% for e3, and 9.4% vs. 7.7% for e4. Individuals with e3e4 and e4e4 genotypes had higher total (P = 0.023) and LDL cholesterol levels (P = 0.04) than individuals with other genotypes. There were no differences in lipid parameters between the subjects with the apoA1-GG genotype and subjects with AG or AA genotypes. However, univariate analysis revealed no association between risk genotypes (e3e4 and e4e4 genotypes) of apoE and CAD risk (OR = 1.1; 95% CI = 0.6-2.1, P = 0.8) as well as no association between the GG genotype and CAD risk (OR 0.7; 95% CI = 0.5-1.2, P = 0.19). No evidence for a synergistic interaction between e3e4 plus e4e4 genotypes and apoA1-GG genotype on CAD risk was found (OR = 1.3, 95% CI = 0.6-2.9; P = 0.5). One individual with familial defective apolipoprotein B-100 (Arg3500Gln) was found in each group. In conclusion, the apoE gene polymorphism affected the total and LDL cholesterol levels, whereas neither the apoE gene polymorphism nor the apoA-1 gene promoter polymorphism were shown to be independent risk factors for CAD in Slovenia.