We now recognize that not all breast cancers are the same. Different characteristics in gene expression profiles result in differential clinical behavior. With the use of gene microarrays, different subtypes of breast cancer have been characterized. These subtypes include the basal, the ERBB2+, and the luminal A, B and C subtypes. The importance of these different subtypes lies in the fact that they differ in clinical outcome, with the basal and ERBB2+ subtypes having the worst prognosis and the luminal A group having the best prognosis. However, identification of these subtypes is still not clinically used. Other strategies for evaluating tumors in a clinical setting have been developed using smaller sets of genes. One such strategy is the 21-gene assay (Oncotype DX), which is currently in commercial use in the USA. One advantage of this test is the use of paraffin-embedded blocks instead of previous methods, which required fresh frozen tissue. Oncotype DX has been shown to predict 10-year distant recurrence in patients with estrogen receptor-positive, axillary lymph node-negative breast cancer. This genomic assay has also been shown to predict chemotherapy and endocrine therapy response. Large, prospective, randomized clinical trials are currently underway using this genomic test. Other similar tests are also finding their way in clinical practice. A 70-gene assay, which has been developed by a group in The Netherlands, is currently being used as a tool to assign treatment in women with early stage breast cancer. In the near future, clinical decisions will most likely be dictated by the genetic characteristics of the tumor, with the clinical characteristics becoming less important. Tailoring our treatment based on individual tumor characteristics will help us develop better therapeutic strategies and save many of our patients from receiving unnecessary toxic therapy.