The pathogenesis of CAD is similar in man and woman, yet some risk factors have a greater impact on the CAD risk in woman than in man. In this study we assessed the effect of the apoE gene polymorphism on lipid metabolism and risk for CAD in women younger than 65 years (premature CAD). In a cross-sectional case-control study, 147 female Caucasian patients with premature CAD (confirmed by coronarography) were compared with a control group of 114 healthy Caucasian women. The apoE allele frequencies of patients vs. controls were 5.1% vs. 5.7% for 2, 85.4% vs. 83.3% for 3, and 9.5% vs. 11% for epsilon4. The subjects with epsilon2/3 genotype had statistically significantly higher triglycerides levels than the subjects with epsilon3/3 genotype (2.23 +/- 2.13 mmol.L(-1) vs. 1.73 +/- 0.84 mmol.L(-1); p<0.05). Logistic regression analysis revealed no association between risk genotypes (3/4 and 4/4) of the apoE gene polymorphism and CAD risk (OR 0.9; 95% CI 0. 5-1.7, P=0.7). We observed metabolic clustering of diabetes mellitus, arterial hypertension, higher BMI and triglycerides, and lower HDL cholesterol in the CAD group compared to the control group. Arterial hypertension, diabetes, HDL cholesterol level, and BMI were independent risk factors for premature CAD in female population, whereas, the risk genotype of the apoE gene polymorphism was not. In conclusion, in Slovene women risk genotypes of the apoE gene polymorphism are not associated with premature CAD; a metabolic clustering of diabetes, HDL, triglycerides and arterial hypertension is frequently present in Caucasian women with premature CAD.