Plasmalogens are targeted by hypohalous acids resulting in the production of 2-chlorofatty aldehydes, 2-bromofatty aldehydes and chlorohydrin species of lysophosphatidylcholine. These novel lipids may have important roles in the pathophysiological sequelae of cardiovascular diseases as well as serve as biomarkers of cardiovascular disease. Accordingly, the discovery of these new lipid species have required the development of techniques for their purification and quantification. Thin layer chromatography, high performance liquid chromatography (LC) and gas chromatography (GC) of these lipids and their derivatives have provided a battery of tools for their analyses. These lipids have been quantified using flame ionization detection (FID) and mass spectrometry (MS).