Gene expression profiling is enabling scientists to understand the heterogeneous nature of breast cancer on a genomic level. Several gene expression profiles for breast cancers have emerged in the initial studies and appear to be generally concordant in their ability to predict poor outcome. Of these profiles, the Oncotype Dx and Mammaprint assays are the best validated and are commercially available. Their role in clinical practice is being refined through ongoing clinical trials. Other efforts are directed at determining host factors that might help identify prognosis as well as response and toxicity of therapy. It is expected that availability of these types of analyses will only increase in the future. It will be imperative that such assays be well validated and have implications for how to modify care for the individual patient.