Several halogenated alkenes are metabolized in part to cysteine S-conjugates, which are mitochondrial toxicants of kidney and, to a lesser extent, other organs. Toxicity is due to cysteine S-conjugate β-lyases, which convert the cysteine S-conjugate into pyruvate, ammonia and a reactive sulphur-containing fragment. A section of the human population is exposed to halogenated alkenes. To understand the health effects of such exposure, it is important to identify cysteine S-conjugate β-lyases that contribute to mitochondrial damage. Mitochondrial aspartate aminotransferase [Cooper, Bruschi, Iriarte and Martinez-Carrion (2002) Biochem. J. 368 , 253–261] and mitochondrial branched-chain aminotransferase [Cooper, Bruschi, Conway and Hutson (2003) Biochem. Pharmacol. 65 , 181–192] exhibit β-lyase activity toward S -(1,2-dichlorovinyl)- l -cysteine (the cysteine S-conjugate of trichloroethylene) and S -(1,1,2,2-tetrafluoroethyl)- l -cysteine (the cysteine S-conjugate of tetrafluoroethylene). Turnover leads to eventual inactivation of these enzymes. Here we report that mitochondrial l -alanine–glyoxylate aminotransferase II, which, in the rat, is most active in kidney, catalyses cysteine S-conjugate β-lyase reactions with S -(1,1,2,2-tetrafluoroethyl)- l -cysteine, S -(1,2-dichlorovinyl)- l -cysteine and S -(benzothiazolyl- l -cysteine); turnover leads to inactivation. Previous workers showed that the reactive-sulphur-containing fragment released from S -(1,1,2,2-tetrafluoroethyl)- l -cysteine and S -(1,2-dichlorovinyl)- l -cysteine is toxic by acting as a thioacylating agent – particularly of lysine residues in nearby proteins. Toxicity, however, may also involve ‘self-inactivation’ of key enzymes. The present findings suggest that alanine–glyoxylate aminotransferase II may be an important factor in the well-established targeting of rat kidney mitochondria by toxic halogenated cysteine S-conjugates. Previous reports suggest that alanine–glyoxylate aminotransferase II is absent in some humans, but present in others. Alanine–glyoxylate aminotransferase II may contribute to the bioactivation (toxification) of halogenated cysteine S-conjugates in a subset of individuals exposed to halogenated alkenes.