In order to develop a liquid chromatography/electrospray ionisation tandem mass spectrometry (LC/ESI-MS/MS) method for identification and quantification of polar metabolites of explosives using a triple quadrupole system, the mass spectrometric ionisation and fragmentation behaviour of different nitrophenols, nitro- and aminonitrobenzoic acids, nitrotoluenesulfonic acids, and aminonitrotoluenes was investigated. Due to their different molecular structures, the substances concerned showed a very different ionisation efficiency in the ESI process. Interestingly, 2,4-dinitrobenzoic acid yielded no mass signals in the Q1 scan suggesting a thermal decarboxylation in the ion source, whereas the corresponding 3,5-isomer showed a high ionisation yield. Using negative ionisation polarity, carboxylic, phenolic, and sulfonic acid groups were deprotonated resulting in molecular anions, which could be fragmented in a collision cell. A pronounced dependency of the produced fragment ion series on the kind and position of substituents at the nitrobenzene ring (ortho effects) was observed and exploited for the development of substance-specific detection methods in the multiple reaction monitoring mode. In case of benzoic and sulfonic acids, decarboxylation and desulfonation, respectively, were observed as the most frequent fragmentation reactions. Furthermore, besides loss of NO2, NO fragmentation occurred and preceded a decarbonylation of the benzene ring. The expulsion of the open-shell molecules NO and NO2 led to a variety of distonic radical anions. Copyright © 2006 John Wiley & Sons, Ltd.