This article is available online at http://www.jlr.org M. E. Brousseau. Coronary heart disease (CHD) is a major cause of death and disability in our society, resulting in approximately 450,000 deaths per year in the United States (2009 Heart and Stroke Statistical Update). Numerous population studies have shown that a strong inverse relationship exists between plasma high density lipoprotein cholesterol (HDL-C) concentrations and CHD risk ( 1-4 ). Approximately 50% of men with CHD have a low level of HDL-C, and not elevated low density lipoprotein cholesterol (LDL-C), as their primary lipid abnormality ( 5 ). In fact, a study in men has shown that a low level of HDL-C better distinguishes CHD status than a high level of LDL-C ( 6 ).Abstract A low level of HDL-C is the most common plasma lipid abnormality observed in men with established coronary heart disease (CHD). To identify allelic variants associated with susceptibility to low HDL-C and CHD, we examined 60 candidate genes with key roles in HDL metabolism, insulin resistance, and infl ammation using samples from the Veterans Affairs HDL Intervention Trial (VA-HIT; cases, n = 699) and the Framingham Offspring Study (FOS; controls, n = 705). VA-HIT was designed to examine the benefi ts of HDL-raising with gemfi brozil in men with low HDL-C ( ≤ 40 mg/dl) and established CHD. After adjustment for multiple testing within each gene, single-nucleotide polymorphisms (SNP) signifi cantly associated with case status were identifi ed in the genes encoding LIPC (rs4775065, P < 0.0001); CETP (rs5882, P = 0.0002); RXRA (rs11185660, P = 0.0021); ABCA1 (rs2249891, P = 0.0126); ABCC6 (rs150468, P = 0.0206; rs212077, P = 0.0443); CUBN (rs7893395, P = 0.0246); APOA2 (rs3813627, P = 0.0324); SELP (rs732314, P = 0.0376); and APOC4 (rs10413089, P = 0.0425). Included among the novel fi ndings of this study are the identifi cation of susceptibility alleles for low HDL-C/CHD risk in the genes encoding CUBN and RXRA , and the observation that genetic variation in SELP may infl uence CHD risk through its effects on HDL. -Peloso, G.