Breast cancer is one of the leading causes of death in women worldwide. During the last decade, great developments in our understanding of breast cancer at the molecular level have arisen from microarray data. Molecular profiling has supported the notion that breast cancer is not a simple disease with a single tumorigenic pathway but a rather heterogeneous one. Gene expression studies have identified and validated the existence of different breast cancer subtypes whose signatures correlate with the clinical outcome. Therefore, the identification of gene expression patterns has become a key issue in understanding the biological diversity of breast tumors, leading to new hope for diagnosis, prognosis, and future treatment. This chapter is a selection of some of the key results that have contributed to the advance toward this end.