Cancer is a heterogeneous disease with wide-ranging subsets of patients who have different prognoses and who respond differently to treatments. Accordingly, deciding the best treatment strategy has become a priority in cancer care. The development of microarray technology over the last decade has caused great excitement, with the promise that these new tools may provide molecular signatures to help predict patient outcome and direct therapeutic approaches. Here, we describe the different types of microarrays available and discuss their pros and cons from a clinical perspective, with respect to breast cancer.