Apolipoprotein (apo)A-II is an abundant human plasma protein primarily in high-density lipoproteins (HDL) but also in very low density lipoproteins (VLDL) and chylomicrons. Despite a large literature, its physiological functions remain ambiguous and widely debated. For example, it has been postulated to play both beneficial and detrimental roles in cardiovascular disease (CVD) development. We believe that apoA-II functions quite differently than other apolipoproteins, which tend to act directly as a co-factor or ligand. We hypothesize that apoA- II impacts both HDL and VLDL metabolism indirectly by altering the lipoprotein proteome and/or affecting the conformation and function of co-residing proteins. Our work shows that apoA-II can stimulate HDL to promote cholesterol efflux from cells, but only when apoA-I is present. This is important because HDL cholesterol efflux proficiency is a better predictor of cardiovascular disease (CVD) than its plasma levels. We also found that apoA-II impacts the VLDL proteome and suspect that this underlies delayed VLDL lipolysis and/or receptor mediated clearance when apoA-II is elevated. Hypertriglyceridemia and delayed post- prandial remnant clearance is an important CVD risk factor. We will define the mechanism for apoA-II’s potentiation of HDL-mediated cholesterol efflux by testing its effects on apoA-I structure using innovative structural techniques including cryo-electron microscopy. An important goal will be to identify the apoA-II sequences responsible with an eye toward developing cholesterol efflux boosting therapeutics. Using human proteins in human plasma- based experiments, we will also determine how apoA-II affects the composition and structure of other VLDL proteins and assess the consequences with respect to activation of lipoprotein lipase and binding to cell surface receptors responsible for its plasma clearance. With a full mechanistic understanding of these effects, it may be possible to derive apoA-II based therapeutic approaches that minimize the protein’s deleterious effects while optimizing benefits for CVD and possibly other metabolic diseases.