This chapter summarizes recently developed gas chromatography–mass spectrometry (GC-MS) techniques for the measurement of lipid peroxidation in tissues. GC–MS methods for the identification of peroxidation products have not been applied to phospholipids with one exception. The key to the methods described in the chapter is a mild transesterification procedure that allows a simple and direct chemical identification and semiquantitative measurement of phospholipid or other glyceroester peroxide products by GC–MS. The method can be simply extended to full quantitation with the use of isotopically labeled internal standards. The method uses sodium borohydride reduction of the hydroperoxides and trimethylsilyl (TMS) derivatives of hydroxy fatty acid esters. The chapter also discusses transesterification technique to form pentafluorobenzyl (PFB) esters and negative ion chemical ionization (NICI) GC–MS that provide several advantages compared to analyses with methyl esters. Lipid peroxides are detected not only in vitamin E deficiency, but also in normal nutritional states. The PFB NICI method can detect and identify lipid peroxides in animals raised on lab chow diets. The chapter also discusses electron ionization (EI) GC-MS methods that allow identification of the contribution of singlet oxygen-mediated reactions during damage to tissues.