Because of the inability to predict and quantify the risk of idiosyncratic adverse drug reactions (IADRs) and because reactive metabolites as opposed to the parent molecules from which they are derived are thought to be responsible for the pathogenesis of some IADRs, procedures (reactive metabolite trapping and/or covalent binding) are being incorporated into the discovery screening funnel early on to assess the risk of reactive metabolite formation. Utility of the methodology in structure–toxicity relationships and scope in abrogating the formation reactive metabolites at the lead optimization stage are discussed in this chapter. Interpretation of the output from reactive metabolite assessment assays, however, is confounded by the fact that many successfully marketed drugs are false positives. Therefore, caution must be exercised in deprioritizing a compound based on a positive result, so that the development of a useful and potentially profitable compound will not be unnecessarily halted. Risk mitigation strategies (e.g. competing detoxication pathways, low daily dose, etc.) when selecting reactive metabolite positive for clinical development are also discussed.