Analyses of molecular species of phospholipids containing choline (Ch), such as phosphatidylcholine (PC) and sphingomyelin (SM), are reported. Neutral loss scanning was applied for the selective detection of these lipids using a quadrupole‐linear ion trap mass spectrometer. By using ammonium formate as an elution buffer, both PC and SM were detected as [M+HCOO]⁻ ions in the negative ion mode. Upon collisional activation, the [M+HCOO]⁻ adduct ions underwent facile elimination of HCO₂, to yield an ion which, in turn, readily underwent collisional‐induced dissociation (CID) to eliminate CH₃ to yield an [M–CH₃]⁻ ion. By selecting the proper conditions for scanning for neutral loss of 60 Da (HCO₂+CH₃), SM species were identified separately from PCs. Further, by selection of this [M–CH₃]⁻ ion as the precursor ion, the identities of the fatty acyl chains of PC species can be effectively obtained by MS³ experiments. Furthermore, by the MS³ analyses of [M–CH₃]⁻ specifically obtained from SM molecules, identification of sphingosine or sphinganine derivatives and their N‐acyl species can also be effectively obtained. This systematic analysis of PCs and SMs by conditional neutral loss scanning, with subsequent analyses by MS³, using a linear ion trap mass spectrometer in the negative ion mode, appears to be a very effective and sensitive method. Further, MS/MS in the positive ion mode at relatively low collision energy was also effective for the identification of positional specificities in individual molecular PC species from their lysoPC‐related fragments. The present paper deals only with qualitative identification of individual molecular species, and the related quantitative studies are now underway. Copyright © 2004 John Wiley & Sons, Ltd.