Gene expression profiling using DNA microarrays allows simultaneous measurement of thousands of mRNA transcripts in a single experiment. Results from gene expression profiling studies have fundamentally altered our view of breast cancer, which is no longer regarded as a single disease but as several molecularly and biologically distinct neoplastic diseases. This technology has also yielded novel diagnostic assays that have started to have an impact on clinical care. This is a rapidly evolving field, and the constraints of space do not allow us to discuss many of the published studies. Therefore, in this review, we will summarize the results of those gene expression studies that are conceptually and practically most important and discuss some of the limitations and the future promise of this technology.