Castration of adult male rats causes dendrites of the spinal nucleus of the bulbocavernosus (SNB) to retract. The neurotrophin brain-derived neurotrophic factor (BDNF) is implicated in mediating these androgenic effects on SNB dendrites. We previously found that castration decreases BDNF mRNA in SNB somata and BDNF protein in proximal SNB dendrites, effects not observed in nearby retrodorsolateral (RDLN) motoneurons. Given that different 5' non-coding exons of BDNF dictate specific subcellular targeting of BDNF mRNA, we set out to identify the specific BDNF transcripts regulated by androgens in SNB motoneurons. We used in situ hybridization to monitor the expression pattern of BDNF transcripts containing non-coding exons I, II, IV, and VI in SNB and RDLN motoneurons in gonadally intact and castrated male rats. While androgen-insensitive RDLN motoneurons expressed all four isoforms, SNB motoneurons contained low levels of BDNF exon IV and little, if any, BDNF exon I. Expression of BDNF isoforms containing exon II and VI was comparable in the two groups of motoneurons. Two weeks after castration, BDNF isoforms containing exon VI were significantly decreased in SNB motoneurons in an androgen-dependent manner, but unaffected in RDLN motoneurons. Because exon VI promotes dendritic localization of BDNF mRNA in other systems, androgens may regulate the dendrites of SNB motoneurons by altering expression of BDNF isoforms, thereby impairing targeting of BDNF protein to dendrites to regulate local synaptic signaling and dendritic structure.