Breast cancer is a common disease in the population. Contrary to public perception, it is a heterogeneous disease with varying morphology, prognosis and response to therapy. The pathological analysis is at the heart of information provided to surgeons and oncologists to plan further management. The pathologist is increasingly asked to test for biomarkers that provide prognostic and predictive information to direct treatment. Staining cancers for ER, PgR and HER2 has become routine and it is likely that addition of other biomarkers including 'basal markers', VEGF and growth factor receptors such as HER1 (EGFR) will soon follow. Microarray based genomic, transcription and proteomic methods are changing our classification systems and identifying novel targets for the development of new therapeutics. It is important for pathologists to appreciate and embrace the new developments as they will impact on daily clinical practice and require accurate assessment of biomarkers to determine treatment options as part of multidisciplinary teams.