Advances in our understanding of the molecular mechanisms underlying breast cancer have identified a considerable number of new molecular targets that may have significant roles in tumor behavior. The rapid and effective transition of these novel, preclinical scientific observations through into the clinic is described as translational research. Tumor markers are an important area of translational research, since they introduce the possibility of identifying groups of patients who possess particular diagnostic or prognostic characteristics. It is important that advances in translational breast cancer research are reviewed in order to determine how they may influence treatment. As part of this process, it is particularly important to identify how these advances may be rationally evaluated through the design of clinical trials, thereby ensuring that the resulting data are sufficiently robust in order to inform and direct clinical decision making. In this way, the treatments available should be efficiently and actively revised to incorporate new concepts of diagnosis, prognosis and treatment, to the benefit of women with breast cancer.