Fish is a source of long-chain omega-3 polyunsaturated fatty acids (LC n-3 PUFA) and methylmercury, a toxic heavy metal, with opposite effects on cardiovascular disease risk and cognitive decline. Besides diet, the apolipoprotein E (APOE) genotype may affect LC n-3 PUFA and mercury concentrations in the body, but the evidence is inconsistent. The subjects were 1159 men aged 42-60 years, examined in 1984-1989. ANCOVA and linear regression were used in the analyses. The mean ± SD concentrations of serum eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA) were 1.57 ± 0.82, 0.55 ± 0.10 and 2.45 ± 0.75%, respectively. There were no differences in LC n-3 PUFA concentrations between APOE4 carriers and non-carriers (P-values ≥ 0.60). The mean ± SD hair mercury concentration was 1.55 ± 1.3 µg/g. The concentrations were slightly higher in APOE4 carriers vs. non-carriers (difference 0.16 µg/g, 95% confidence interval = 0.01-0.32,P = 0.04). Overall, fish consumption was associated with higher hair mercury and serum EPA and DHA concentrations, but no differences in the associations were found between APOE4 carriers and non-carriers (P-interactions ≥ 0.30). Hair mercury, but not serum LC n-3 PUFA concentrations, were higher in APOE4 carriers vs. non-carriers. However, as no differences were found in the associations of fish intake with LC n-3 PUFA and mercury concentrations, the results could be due to differences in mercury accumulation.