Atherosclerosis is characterized by the accumulation of both lipoprotein-derived lipids and inflammatory cells in the affected vascular wall that results in a state of heightened oxidative stress and that is reflected by the accumulation of oxidized lipoproteins. Circulating oxidized low-density lipoprotein (oxLDL) is used as a surrogate marker for coronary artery disease, although the 'escape' of oxLDL from the vessel wall is hindered by the large size of this lipoprotein and its specific retention by the extracellular matrix. Also, the oxidation of lipoproteins in human atherosclerotic lesions is not limited to LDL. In fact, the lipids of all classes of lipoproteins are oxidized to a comparable extent. Examining the fate of lipid hydroperoxides, the primary lipid peroxidation products, in high-density lipoproteins (HDL) undergoing oxidation, revealed that they become reduced to the corresponding alcohols by specific Met residues of apolipoprotein A-I (apoA-I) and apoA-II. As a consequence, Met residues in apoA-I and apoA-II become selectively and consecutively oxidized to their respective Met sulfoxide (MetO) forms that can be separated by HPLC. This review describes the characterization of specifically oxidized HDL with an emphasis on MetO formation, the structural and functional consequences of such oxidation, and the potential utility of specifically oxidized HDL as a surrogate marker of atherosclerosis.