Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family of secreted proteins and has important functions in the peripheral and central nervous systems (CNS). Its gene organization is complex, comprising four untranslated exons, each with an associated promoter. We have examined the expression of the four untranslated exons in direct comparison to one another and to the fifth BDNF coding exon by in situ hybridization. Other studies have examined untranslated exon expression in several brain regions in response to specific stimuli; however, this is the first detailed study to describe endogenous exon 1-4 expression throughout the adult mouse brain at baseline conditions. The differential expression of the four untranslated exons seen throughout the brain indicates a complex regulation of BDNF. Copyright 2005 Wiley-Liss, Inc.