Background: Epidemiological studies suggest that apolipoprotein E (apo E) polymorphisms influence the plasma lipoprotein levels, resulting in a higher risk for atherosclerotic disease in subjects with E4 allele.Methods and Results: Using high-resolution ultrasound method, we investigated the association between apo E polymorphism and early atherosclerosis evaluated by carotid intima-media thickness (IMT) and flow-mediated dilatation (FMD) of brachial artery during reactive hyperemia in 95 middle-aged healthy Japanese men (31 to 69 years; mean ± SD age, 50 ± 8 years). The allele frequencies of E2, E3 and E4 were 0.053, 0.842 and 0.105, respectively. Serum cholesterol and LDL-cholesterol levels (221 ± 32 and 143 ± 28 mg/dl, respectively) in subjects with E4 allele were highest, and those (187 ± 27 and 110 ± 20 mg/dl, respectively) in subjects with E2 allele were lowest (p < 0.04 and p < 0.02, respectively). The mean max common carotid IMT (0.76 ± 0.22 and 0.76 ± 0.22 mm, respectively) in subjects with E2 and E4 alleles were greater than that (0.64 ± 0.14 mm) in subjects with E3 allele (p < 0.01). However, brachial FMD (6.9 ± 2.9 and 6.2 ± 3.3%, respectively) in subjects with E2 and E4 alleles were relatively, but not significantly, lower than that (7.8 ± 4.2%) in subjects with E3 allele (p = 0.24). By univariate analysis, carotid IMT was positively correlated with age (R = -0.49, p < 0.01), and negatively correlated with HDL-cholesterol (R = -0.35, p < 0.01). On the contrary, brachial FMD was negatively correlated with age (R = -0.39, p < 0.01) and cigarette smoking (R = -0.23, p < 0.05). Moreover, carotid IMT and brachial FMD were negatively correlated (R = -0.26, p < 0.02). By multivariate analysis, carotid IMT was associated with age and HDL-C, but not with apo E phenotype.Conclusions: Age was a strong predictor in both early carotid atherosclerosis and endothelial dysfunction of the brachial artery in middle-aged healthy Japanese men.