Recent advances in DNA microarray technology have enabled the simultaneous evaluation of thousands of genes and the subsequent generation of massive amounts of biological data relevant to injury or diseases of the central nervous system (CNS). This technology has the potential to bridge the gap between molecular and systems neuroscience by efficiently revealing the discrete molecular aspects underlying the perturbations of complex systemic insults such as those resulting from traumatic brain injury (TBI). One of the more intriguing and as of yet not understood aspects of TBI that can be efficiently explored with DNA microarrays, is the sequence of molecular events that results in pronounced cell death in specific areas of the brain. The elucidation of these changes in gene expression underlying the mechanism of cell death following brain injury is of central importance in the design of future therapeutic agents. This review focuses on the technical aspects of microarray manufacture (photolithography, microspotting, and ink jet technology) and their utility in elucidating the molecular sequelae of brain injury.