A simple capillary zone electrophoresis (CZE) method was used to characterize native, in vitro oxidized and glycated human high-density lipoprotein (HDL) particles. Both native and in vitro oxidized HDL capillary electrophoresis (CE) profiles showed a major peak, but the oxidized HDL particles had higher effective mobilities. The in vitro glycated HDL particles showed a major peak and one or two minor peaks. The effective mobility of the major peak of glycated HDL was similar to that of the major peak of native HDL, whereas the effective mobilities of the two minor peaks were much lower. For the analysis of HDL phospholipids, a solid phase extraction procedure was optimized and a LC ESI-MS method was developed. Several possible HDL phospholipid molecular species including phosphatidylcholine (PC 16:0/18:2, 16:0/18:1, 18:0/18:2 and 18:0/18:1), sphingomyelin (SM 16:0) and lyso-phosphatidylcholine (lysoPC 16:0 and 18:0) were found. It appeared that the ion intensity ratios of hydroperoxy-PC or epoxyhydroxy-PC (16:0/hydroperoxy-18:2 or 16:0/epoxyhydroxy-18:2, m/z 790.4) and trihydroxy-PC (16:0/trihydroxy-18:2, m/z 808.3) relative to PC (C16:0/C18:2, m/z 758.5) were higher for oxidized HDL than for native and glycated HDL. It should be helpful to use both CZE and LC ESI-MS methods for analyzing high-density lipoproteins from patients of cardiovascular disease. Their combination may be also useful for further studies concerning the role of oxidized and glycated HDLs in the development of atherosclerosis.