The invention provides methods of screening a mammalian subject to determine if the subject is at risk to develop, or is suffering from, cardiovascular disease. The methods comprise detecting an amount of at least one biomarker in a biological sample, or HDL subfraction thereof, from the subject, and comparing the detected amount of the biomarker to a predetermined value, where a difference between the detected amount and the predetermined value is indicative of the presence or risk of cardiovascular disease in the subject. In some embodiments, the biomarker comprises at least one of ApoC-IV, Paraoxonase 1, C3, C4, ApoA-IV, ApoE, ApoL1, C4B1, Histone H2A, ApoC-II, ApoM, Vitronectin, Haptoglobin-related protein, and Clusterin, or combinations thereof.