Glutathione conjugation is widely recognized as an important detoxification mechanism for a variety of electrophilic xenobiotics. However, several pathways have been defined by which glutathione conjugates may be toxic. One proposed route of toxicity occurs when glutathione conjugation does not completely eliminate the toxicity of a xenobiotic. The toxicity of thioether conjugates of quinones was investigated as an example of toxicity by this route. The N-acetylcysteine conjugate of the quinone menadione (2-methyl-1,4-naphthoquinone) was found to damage isolated rat renal epithelial cells primarily by inducing oxidative stress. Interestingly, the glutathione conjugate of menadione was not toxic to isolated rat renal epithelial cells because a novel intramolecular cyclization reaction destroys the quinone nucleus. Another route of glutathione conjugate toxicity involves metabolism to the cysteine conjugate followed by activation to a reactive intermediate by cysteine conjugate {dollar}\beta{dollar}-lyase. Halogenated alkenes are examples of compounds toxic through this route. The toxicity of S-(1,2,3,4,4-pentachlorobutadienyl)-L-cysteine (PCBC), the cysteine conjugate of hexachlorobutadiene, is associated with a rise in cytosolic calcium. Work presented here suggests that this rise is important in the toxicity since buffering this rise with cell permeant Ca{dollar}\sp{lcub}2+{rcub}{dollar} chelators is protective. The toxicity was not associated with an activation of catabolic enzymes; however, it did appear to be associated with oxidative damage. In addition, the oxidative damage appeared to be related to deregulation of cytosolic Ca{dollar}\sp{lcub}2+{rcub}{dollar}. Mitochondria have been proposed to be a critical target of haloalkene thioether conjugates. In isolated rat renal mitochondria these conjugates induced an inner membrane permeability transition characterized by collapse of the membrane potential, release of Ca{dollar}\sp{lcub}2+{rcub}{dollar}, and oxidation of pyridine nucleotides. All of these effects were blocked by treatments known to inhibit the induction of the permeability transition. However, a nonmetabolisable form of PCBC also induced the same effects, suggesting that this process does not require the activation of the conjugates to a reactive electrophile through the {dollar}\beta{dollar}-lyase pathway.