We examined sex differences in the transcriptomes of hypothalamus, pituitary gland, and cortex of male and female mice using serial analysis of gene expression. In total 940,669 tags were sequenced. In hypothalamus, 3 transcripts are differentially expressed by gender, including growth hormone (neuromodulation) and 3beta-hydroxysteroid dehydrogenase-1 (steroidogenesis). In pituitary gland, 43 transcripts are differentially expressed, including RAS guanyl-releasing protein 2 (cell signaling), ornithine transporter (mitochondrial transport), H3 histone family 3B (chromatin structure), heterogeneous nuclear ribonucleoprotein U (chromatin remodeling), NADH dehydrogenase (mitochondrial oxidative phosphorylation), neuronatin (cell differentiation), and ribosomal protein S27a (protein metabolism). EST X (inactive)-specific transcript antisense is expressed at a higher level in the three female organs, whereas growth hormone and NADH dehydrogenase are expressed at higher levels in female cortex. Thus, the current study has characterized key sexual dimorphisms in the transcriptomes of the hypothalamus, pituitary, and cortex.