Recent progress in genomics and proteomics technologies has created a unique opportunity to significantly impact the pharmaceutical drug development processes. The perception that cells and whole organisms express specific inducible responses to stimuli such as drug treatment implies that unique expression patterns, molecular fingerprints, indicative of a drug's efficacy and potential toxicity are accessible. The integration into state-of-the-art toxicology of assays allowing one to profile treatment-related changes in gene expression patterns promises new insights into mechanisms of drug action and toxicity. The benefits will be improved lead selection, and optimized monitoring of drug efficacy and safety in pre-clinical and clinical studies based on biologically relevant tissue and surrogate markers.