Polymorphisms of the apolipoprotein E gene (ApoE) have been associated with health and longevity. Numerous studies have linked ApoE to health outcomes including cardiovascular disease and mortality, but far fewer studies have examined the relationship of ApoE to other biological markers of health. This study investigates the relationship between ApoE and mortality, as well as ApoE and a set of biomarkers related to cardiovascular and immune function, in a population-based sample of Taiwanese adults ages 54+. ApoE ɛ2 carriers were less likely to have at-risk levels of high-density lipoprotein (HDL-C) and total cholesterol (total-C) than non-carriers (odds ratio [OR] 0.45, 95% confidence interval [CI] 0.25–0.83 and OR 0.45, 95% CI 0.29–0.71, respectively). ApoE ɛ4 carriers were less likely to have elevated levels of C-reactive protein (CRP) than non-carriers (OR 0.62, 95% CI 0.39–0.96). ApoE genotype was not, however, associated with mortality after 8 years of follow-up. Our findings confirm the association between ApoE ɛ2 and cholesterol levels, suggesting a potential protective effect of ApoE ɛ2 on blood lipids. They also contribute to reports on the relationship between ApoE ɛ4 carrier status and lower CRP levels.