The analysis of 1-hexadecyl-2-acetyl-glycerophosphocholine (platelet activating factor, PAF) by negative ion and normal-phase liquid chromatography/tandem mass spectrometry (LC/MS/MS) was investigated as an alternative technique to the currently used gas chromatography/MS and positive ion LC/MS/MS procedures. The positive ion [M + H]+ derived from PAF and generated by electrospray ionization is abundant, but the potential presence of isobaric 1-octadecanoyl-2-lyso-glycerophosphocholine (stearoyl-lyso-GPC) and 1-hexadecanoyl-2-formyl-glycerophosphocholine (PFPC) in biological samples limits the use of the most abundant collision-induced decomposition (CID) transition (formation of the phosphocholine ion, m/z 524-->184) if chromatographic separation is not achieved. Less abundant CID product ions, such as loss of the neutral ketene molecule derived from the respective fatty acyl groups, provide the requisite specificity, but the intensity of these transitions yields a signal-to-noise ratio that greatly diminishes the analytical sensitivity. With negative ion LC/MS/MS, however, the molecular anions [M - 15]- derived from PAF, stearoyl-lyso-GPC and PFPC decompose to the carboxylate anions at m/z 59, 283 and 255, respectively, permitting discrimination of these isobaric molecules even without chromatographic separation. In addition, the CID of [M - 15]- was favorable, yielding ion currents of sufficient intensity to permit the measurement of PAF when isolated from small quantities of biological material. With the use of a stable isotopically labeled variant of PAF and isotope dilution, negative ion LC/MS/MS was found to measure PAF reliably even in the presence of the isobaric stearoyl-lyso-GPC and permitted the use of non-chlorinated mobile phases for normal-phase high-performance LC.