Breast cancer is a heterogeneous disease, encompassing a wide variety of histological types and clinical behaviours. Current histopathological classification systems for breast cancer are based on descriptive entities that are of prognostic significance. Few predictive biomarkers are currently available. High throughput molecular technologies are reshaping our understanding of breast cancer and a molecular taxonomy that has stronger predictive power is slowly emerging. Novel therapeutic targets and prognostic/predictive gene signatures have been identified. This review will address the contribution of molecular methods to our understanding of breast cancer and its precursors, their use in breast cancer translational research and their impact on diagnostic breast cancer histopathology.