Patients exhibit a range of responses to drug treatment owing to individual genetic variation and biology. A deeper understanding of the human genome, enabled by increasingly powerful technologies to measure both its genes and gene products, has unleashed the concept of tailoring therapy to the individual patient upon pharmaceutical and clinical sciences. The successful application of personalized medicine depends upon the discovery and development of biomarkers. Biomarkers that either indicate pharmacodynamic effects or constitute predictive measures of individual patient responses can support dose selection and/or help determine therapeutic options. The development of biomarkers for clinical testing and validation can be facilitated by the use of ex vivo systems utilizing clinically relevant human tissues for the discovery of biomarkers of drug activity before first in human (FIH) studies. In this review we discuss the uses of ex vivo systems for both disease tissues and surrogate normal tissues to provide mechanistic insights into drug action and for the purpose of identifying candidate biomarkers.