The present paper provides a summary of the collision-induced dissociation of protonated and deprotonated phase II metabolites of drugs and pesticides. This overview is based on published literature and unpublished data from the authors. In particular, glutathione conjugates and their biotransformation products are discussed in detail. In addition, the fragmentation of the major classes of conjugates, i.e. glucuronides, glucosides, malonylglucosides, sulfates, acetates, methyl and glycine conjugates, is reported. Collision-induced dissociation, as studied by tandem mass spectrometry, allows the rapid identification of the type of conjugate, whereas the exact conjugation site can in general be determined only by additional NMR experiments.