This data provides the basis for further research to delineate the role of novel genes in XRT-induced CNS injury. JAK3 will be studied as a potential neuro-protective target from XRT injury.The possibility of damaging the central nervous system (CNS) is a major problem in clinical radiation treatment (XRT). Using cDNA microarray, we studied global gene expression in mouse brain within 24 h following clinically relevant doses of XRT.Early response of mouse brain to XRT is a complex process that involves dose- and time-dependent expression of hundreds of genes and modulates different molecular functions and pathways. Genes involved in signal transduction, metabolism, structural proteins, transcription, and cell cycle were modulated by XRT in mouse brain. Using real time PCR, we confirmed changes in expression of DNA fragmentation factor, beta subunit, nuclease sensitive element binding protein 1, Janus kinase3 (JAK3), and Telomeric repeat binding factor 1. Upregulation of JAK3 expression was demonstrated by immunohistochemistry.