In both mice and humans, males and females exhibit differences in behavior and response to neurological and psychological diseases that are linked to the cortex and hippocampus. The perinatal exposure of males to testosterone secreted by the testes creates alterations in neural structures and behaviors that can persist throughout their lives; however, the molecular mechanisms that underlie the actions of sex steroids to produce these lasting changes are still unclear. Given that regulation of gene expression is a primary mechanism whereby sex steroids exert changes to an organism, I sought to identify genes expressed at different levels between the sexes in the cortex and hippocampus and to determine the effect of testosterone on expression of these genes. Using gene expression microarrays and RT-qPCR, I identified genes that are differentially expressed between the sexes in the neonatal mouse cortex and hippocampus; however, whether perinatal testosterone is regulating these differences remains unclear.