The low incidence of idiosyncratic drug-induced liver injury (DILI), together with the lack of a reliable diagnostic biomarker and robust preclinical and in vitro toxicology test systems for the condition have limited our ability to define the mechanisms of DILI. A notable exception is acetaminophen hepatotoxicity, which is associated with the formation of a well-characterized and highly reactive intermediate metabolite, N-acetyl-p-benzoquinone imine. However, studies have also suggested a role for the host immune response and variation in the expression of the lymphocyte CD44 gene in the pathogenesis of acetaminophen hepatotoxicity. A careful review of the laboratory, clinical and histological phenotype of patients with DILI can provide potential clues to the mechanisms of disease pathogenesis, as observed with fialuridine and valproate hepatotoxicity. In addition, the use of transcriptomic and genomic approaches in patients with well-characterized DILI has provided important insights into the involvement of the host immune response in the pathogenesis of hepatotoxicity associated with the administration of flucloxacillin, lumiracoxib or ximelagatran. This Review highlights new developments regarding the potential role of reactive metabolites, mitochondrial toxicity, host immune-response pathways and biliary transporters in the etiopathogenesis of DILI. Going forward, a bedside-to-bench approach could improve our understanding of the mechanisms and risk factors for DILI.