Under the action of free-radical reaction initiators on membrane phospholipids, complex processes are taking place in both hydrophobic and hydrophilic parts of the phospholipids. Realization of these processes results in a mixture consisting of the initial lipids and their peroxidation and fragmentation products. Identification of compounds in such mixtures requires analytical methods of high sensitivity, reproducibility and accuracy to be applied. These properties are characteristic of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method. In the studies of radiation-induced free-radical transformations of phosphatidylglycerol, the MALDI-TOF MS in combination with thin layer chromatography (TLC) has been shown to be able to detect and identify products of free-radical transformations taking place in both hydrophilic and hydrophobic parts of the phospholipid. Thus, the MALDI-TOF MS can serve as a suitable analytical tool to investigate free-radical transformations of lipids.