Breast cancer is a complex genetic disease characterized by the accumulation of multiple molecular alterations. Routine clinical management of breast cancer relies on clinical and pathological factors, however. These seem insufficient to reflect the whole clinical heterogeneity of tumours and are less than perfectly adapted to each patient. Recent advances in human genome research and high-throughput molecular technologies have made it possible to tackle the molecular complexity of breast cancer and have contributed to the realization that the biological heterogeneity of breast cancer has implications for treatment. Gene expression profiling of breast cancer has been performed using several approaches. This review will describe the details of gene expression profiling of breast cancer, the different approaches and the impact on clinical management.