Although molecular testing has been increasingly used in clinical practice, the precise diagnosis and prognosis of most human cancers still heavily rely on descriptive histopathological data. Identification of robust molecular markers associated with distinctive morphological parameters will assist in diagnostic and prognostic assessment. On the other hand, the diversity of morphologically identical/similar cancers can be manifested at multiple levels, most importantly at the level of clinical outcome. In the past several years, DNA microarray technology has been widely used in the context of cancer research, resulting in a deluge of new information that can be used to identify molecular alterations common to all tumors as well as signatory profiles unique to a subcategory of cancers. These new findings will very likely transform the clinical management of cancer patients in the near term. This article reviews recent advances in cancer gene expression-profiling results derived from the application of DNA microarray technology, with an emphasis on studies performed on human prostate cancer specimens. We discuss broad issues relevant to cancer expression profiling and attempt to illustrate the rapid pace of novel discoveries using prostate cancer as examples wherever appropriate.