DNA microarrays are capable of measuring the expression of thousands of genes in a single assay. This technology has led to an explosion in global gene expression profiling studies, allowing researchers to more fully explore a multitude of complex biological systems ranging from the yeast cell cycle to the progression of cancer. By analyzing collections of these global profiles, the molecular underpinnings of biological phenomena are being unraveled. It is the goal of this review to address the basic principles of the technology and methodology employed in gene expression profiling with DNA microarrays, and then to highlight recent studies with particular importance for clinical medicine, focusing on cancer.