Shaping and orchestrating the genetic program involved in embryonic modelling of brain structures is a major function played by homeobox containing genes. Recently, analysis of conditional mouse mutants has pointed out additional roles in supporting adult brain functional activities. During a search for novel homeobox genes in the public released genomic sequences derived by the Human and Mouse genome projects, we were able to identify the mouse homologue of the Drosophila brain specific homeobox gene. We named it Bsx and characterized its expression in embryonic and post-natal mouse brain. Interestingly, Bsx shows an expression pattern restricted to a few specific developing brain structures. Pineal gland, telencephalic septum, hypothalamic pre-mammillary body and arcuate nucleus are the only brain structures where we detected Bsx transcriptional activity, which is maintained also after birth. In particular, Bsx might be considered an important molecular marker for early embryonic stages of epiphysis development, being specifically expressed in this neural structure from E9.5 onwards.