Atherosclerosis is associated with dysfunctional HDL, and oxidation of HDL is thought to give rise to HDL becoming dysfunctional. Lipoprotein oxidation represents a complex series of processes that can be assessed by various methods. In general, oxidation mediated by 1-electron or radical oxidants gives rise to lipid hydroperoxides (LOOHs) as the primary product. These LOOHs may then undergo further reactions giving rise to secondary lipid oxidation products and/or oxidation of lipoprotein-associated proteins. Thus, LOOHs specifically oxidize Met residues of apolipoprotein (apo) A-I and A-II (the major proteins of HDL) to MetO. Here we describe an HPLC-based method to detect oxidized HDL containing specifically oxidized forms of apoA-I and apoA-II. This method may be useful to assess the early stages of HDL oxidation in biological samples.