Microarray analysis has emerged as a tool to study the multiple, complex effects of pharmacological treatments on changes in gene expression. Examining innate differences and changes in gene expression in response to ethanol in lines or strains of mice and rats with divergent responses to ethanol has provided important clues toward identifying genes and gene networks involved in vulnerability to high ethanol-drinking behavior. Given this, examining changes in gene expression following chronic ethanol drinking will, presumably, provide information to identify genes and gene networks involved in maintaining this behavior, as well as the consequences of chronic ethanol exposure.