The capillary electrophoresis (CE) separation of different anionic phospholipid classes including phosphatidic acids (PA), phosphatidylserine, phosphatidylinositol, phosphatidylglycerol (PG), and cardiolipin using indirect detection with adenosine monophosphate (AMP) is described. A standard mixture of PAs (C14, C16, and C18) can be separated in 10 min by CE using 5 mM AMP and 100 mM boric acid in 10% water--80% methanol--10% acetonitrile. Although nonionic surfactants such as Brij 35 can improve the CE resolution of PAs, the separation time and the baseline noise are both increased. Optimization of the organic solvent in the running electrolyte is important. Methanol provides faster electroosmotic flow than propanol, and 10% acetonitrile effectively reduces migration time further by a factor of 1.4-2.2, depending on the phospholipid. The concentration limit of detection ranges from approximately 2 to 6 mg/L, and the mass limit of detection is as low as 21 pg. Linearity from 19 to 100 mg/L is established for cardiolipin and C16-PG. Phospholipids in soybean and brain extract samples could be profiled.