Genomics studies are now widely used in toxicology. At APHC, several studies have examined the toxicology of explosives and metals. This work has required collaborative efforts between other organizations, such as the US Army Engineer Research and Development Center at Vicksburg, MS, and the Medical Research Institute of Chemical Defense at Aberdeen Proving Ground, MD. Microarray expression studies have been used to examine the impact of RDX and tungsten alloys on global gene expression with a view to identifying signature profiles of genes specifically related to exposure. In some cases, these signature profiles can contain information that indicates an underlying mode of action of the chemical; this makes the analytical approach and the interpretation of data critical in genomics investigations. Because these large datasets include false positives and difficult to challenge conclusions it is important to have well designed studies that address specific questions.