Dehydration has a profound influence on neuroexcitability. The mechanisms remained, however, incompletely understood. The present study addressed the effect of water deprivation on gene expression in the brain. To this end, animals were exposed to a 24 hours deprivation of drinking water and neuronal gene expression was determined by microarray technology with subsequent confirmation by RT-PCR. As a result, water deprivation was followed by significant upregulation of clathrin (light polypeptide Lcb), serum/glucocorticoid-regulated kinase (SGK) 1, and protein kinase A (PRKA) anchor protein 8-like. Water deprivation led to downregulation of janus kinase and microtubule interacting protein 1, neuronal PAS domain protein 4, thrombomodulin, purinergic receptor P2Y - G-protein coupled 13 gene, gap junction protein beta 1, neurotrophin 3, hyaluronan and proteoglycan link protein 1, G protein-coupled receptor 19, CD93 antigen, forkhead box P1, suppressor of cytokine signaling 3, apelin, immunity-related GTPase family M, serine (or cysteine) peptidase inhibitor clade B member 1a, serine (or cysteine) peptidase inhibitor clade H member 1, glutathion peroxidase 8 (putative), discs large (Drosophila) homolog-associated protein 1, zinc finger and BTB domain containing 3, and H2A histone family member V. Western blotting revealed the downregulation of forkhead box P1, serine (or cysteine) peptidase inhibitor clade H member 1, and gap junction protein beta 1 protein abundance paralleling the respective alterations of transcript levels. In conclusion, water deprivation influences the transcription of a wide variety of genes in the brain, which may participate in the orchestration of brain responses to water deprivation.