Biomarkers are physical, functional or biochemical indicators of physiological or disease processes. These key indicators can provide vital information in determining disease prognosis, in predicting of response to therapies, adverse events and drug interactions, and in establishing baseline risk. The explosion of interest in biomarker research is driving the development of new predictive, diagnostic and prognostic products in modern medical practice, and biomarkers are also playing an increasingly important role in the discovery and development of new drugs. For the full utility of biomarkers to be realized, we require greater understanding of disease mechanisms, and the interplay between disease mechanisms, therapeutic interventions and the proposed biomarkers. However, in attempting to evaluate the pros and cons of biomarkers systematically, we are moving into new, challenging territory.