The published literature is awash with examples of new tissue biomarkers promising to predict responses to therapy in breast cancer patients. However, few, if any, of these progress from the laboratory to the clinic. In this review we discuss some of the reasons for this, illustrating our discussion with a selection of biomarkers which are in development and which may be candidates for clinical application within the next few years (topoisomerase II alpha, epidermal growth factor receptor, AKT, phosphatase and tensin homologue). In particular, we explore how our ever increasing knowledge of molecular and pathway biology is facilitating hypothesis-driven biomarker discovery, and the statistical considerations which need to be addressed in order to validate new candidate biomarkers adequately.