Various analytical techniques have been adopted for the isolation and identification of the oxolipids and for determining their functionality. Gas chromatography in combination with mass spectrometry (MS) has been specifically utilized in analysis of isoprostanes and other low molecular weight oxolipids, although it requires derivatization of the solutes. In contrast, liquid chromatography (LC) in combination with on-line MS has proven to be well suited for analysis of intact oxolipids without (or minimal) derivatization. LC-MS has also been helpful for the identification of lipidomic changes resulting from covalent binding of lipid ester core aldehydes to amino lipids, amino acids, peptides, and proteins. This chapter reviews the use of the above techniques for lipidomic analysis of the autoxidation products of cholesteryl esters and glycerolipids as practiced in the authors' laboratories.