It is sometimes assumed that because the brain is such a complex organ, experimental genomics methods are not directly applicable to neurobiological studies. In fact, it is because the brain and brain process are complex that it is even more important to apply methods that allow large numbers of genes to be monitored across a significant number of experiments. How can we begin to understand the mechanisms underlying various brain functions, and how can we understand what can and does go wrong in disease? How can such tasks be accomplished without being overly costly and time- and labor-intensive? We and others have put DNA microarray technology to work to address a variety of biological problems, and in particular to study the brain and various brain functions. This review provides an overview of how we use DNA microarray technology to identify the genes that are responsible for specific neurological responses, seizure-induced responses, and the unique structures and functions of different brain regions.