The rapid progress in genomics and proteomics technologies creates a unique opportunity for understanding the mechanisms of action and the toxicities of compounds. The application of gene-expression and protein-expression profiling promises to improve the predictive power of safety assessment, resulting in the development of drug candidates with a higher efficacy and a lower toxicity. Additionally, in the later phases of drug development, surrogate markers of treatment efficacy and toxicity can be applied to optimise the monitoring of pre-clinical and clinical studies.