Increasing evidence for phosphatidylcholine hydroperoxide (PCOOH) as a marker of oxidative food deterioration and oxidative diseases has revealed the need for a pure PCOOH standard and a reliable quantification method. Recently, we synthesized the PCOOH isomers 1-palmitoyl-2-(9-hydroperoxyoctadecadienoyl)-sn-glycero-3-phosphocholine, (16:0/9-HpODE PC) and 1-palmitoyl-2-(13-hydroperoxyoctadecadienoyl)-sn-glycero-3-phosphocholine (16:0/13-HpODE PC). Using these standards along with liquid chromatography-tandem mass spectrometry, a reliable quantification method was developed. This mini-review describes these analytical techniques, with a particular emphasis on clinical sample analysis.