Recent advances in gene expression profiling and other "omics" technologies have revolutionized cancer research and hold the potential of also revolutionizing clinical practice. These high-throughout approaches have radically changed our ability to study cells and tissues in a more comprehensive way. Combined with advanced bioinformatics and the possibility to simulate biological processes in computers, this field of "systems biology" allows us to study the organism as a whole entity. This chapter describes the molecular classification and characterization of breast tumors into distinct subtypes by using DNA microarrays and discusses the statistical relationships of the subgroups with clinical features of the disease.