Adverse drug reactions, such as hepatotoxicity, blood dyscrasias and hypersensitivity are a major obstacle for the use and the development of new medicines. Many forms of organ-directed toxicity can arise from the bioactivation of drugs to so-called chemically reactive metabolites, which can modify tissue macromolecules. It is well established that the toxicities of model hepatotoxins, such as acetaminophen, furosemide, bromobenzene and methapyrilene can be correlated with the generation of chemically reactive metabolites, which can be detected by measurement of the irreversible binding of radiolabelled material to hepatic protein and/or the detection of stable phase II metabolites such as glutathione conjugates. The basic chemistry of the reaction of such metabolites with model nucleophiles is relatively well understood. A major challenge is to define how certain reactive intermediates may chemically modify critical proteins and how modification of specific amino acids may alter protein function which in turn may affect cell signalling, regulation, defence, function and viability. This in turn will determine whether or not bioactivation will result in a particular form of drug-induced injury. It is now clear that even relatively simple reactive intermediates can react in a discriminative manner with particular cellular proteins and even with specific amino acids within those proteins. Therefore both non-covalent, as well as covalent bonds will be important determinants of the target protein for a particular reactive metabolite. Mammalian cells have evolved numerous defence systems against reactive intermediates. Sensitive redox proteins such as Nrf-2 recognize oxidative stress and electrophilic agents. This is achieved by chemical modification of cysteine groups within keap-1, which normally forms an inactive heterodimer with Nrf-2. Modification of keap-1 releases Nrf-2 that translocates to the nucleus and effects gene transcription of a number of genes involved in the detoxication of chemically reactive metabolites. Diminution of protein function can occur by either covalent modification of nucleophilic amino acids (e.g. cysteine, lysine, histidine etc.) or oxidation of thiols, which can be reversible or irreversible. In the case of acetaminophen, more than 30 target proteins have been identified and for several of them, corresponding alterations in protein function have been defined in the context of tissue necrosis. Alternatively, protein modification may induce signalling systems which initiate cell death, an immune response or to an altered tissue genotype.