Electrospray ionization combined with tandem mass spectrometry was applied to a study of some representative chlorinated and nitrated isoflavones - potential metabolites of isoflavones in inflammatory cells. Upon collision-induced dissociation of deprotonated [M - H]- ions of these compounds, a number of structurally characteristic product ions were produced. The product ion analysis of 3′- and 8-chlorodaidzein in the tandom mass spectra led to ready differentiation of these isomers. 3-Nitro derivatives of both genistein and daidzein have product ions due to the losses of HNO2 and two OH groups. Chlorinated derivatives of isoflavones were detected in cell-based experiments and their structures were proposed by comparing the tandem mass spectra of their product ions with those of standards. This work provides a suitable analytical basis to aid the characterization of chlorinated and nitrated metabolites in studies in vivo and in vitro. Copyright © 2003 John Wiley & Sons, Ltd.