The relationship between variations in the apoAI-CIII-AIV gene cluster and plasma lipid traits has been recognized for at least 15 years. Most studies have been focused upon the association between plasma triglycerides and a genetic variation present in the 3' untranslated region of the apoC-III gene (SstI polymorphism). Although not all studies showed similar results, this variant is most consistently found in association with plasma triglycerides. The other most interesting DNA variant is the mutation present in the promoter region of the apo A-I gene at position -75 (Msp-AI polymorphism), which has been associated with differences in plasma apoA-I and HDL-cholesterol levels. In this review, we will discuss the most frequent occurring genetic variants in the apoAI-CIII-AIV gene cluster and their impact on plasma lipid traits and associations with increased risk on developing coronary artery disease.