In recent years advances in molecular biology have launched disruptive innovations in breast cancer diagnostics and therapeutics. The advent of genomics has revolutionized our understanding of breast cancer as several different biologically and molecularly distinct diseases. This research has led to commercially available polymerase chain reaction (PCR) and microarray tests that have begun to fundamentally change the way medical oncologists quantify recurrence risk in early stage breast cancer patients. The Genomics era has altered the clinicopathologic paradigm of selecting patients for adjuvant cytotoxic chemotherapy. Sufficiently powered prospective studies are underway that may establish these molecular assays as elements of standard clinical practice in breast cancer treatment. In this article, we review the strengths and limitations of currently available breast cancer-specific molecular tests.