Brain-derived neurotrophic factor (BDNF) is a growth factor belonging to the family of neurotrophins. Although neurotrophins in the male genital organs have been well documented, their role in the biology of these organs is far from clear. In particular, little is known about the influence of sex hormones on neurotrophin expression. In the present study, using immunohistochemistry and enzyme-linked immunosorbent assay (ELISA), we investigated the distribution and tissue concentration of BDNF in the vas deferens and accessory male genital glands in normal and castrated rats. The expression of BDNF mRNA was also investigated. In normal rats, BDNF immunoreactivity was localized in the musculature of the vas deferens and vesicular gland and in the fibromuscular stromal cells of the prostate. In the ventral prostatic lobes, BDNF immunoreactivity was localized in basal, secretory and neuroendocrine epithelial cells. Innervating ganglia and nerves were immunoreactive in all the examined tracts. After castration, BDNF immunoreactivity increased in the musculature of the vesicular gland and in the fibromuscular stromal cells of both dorsal and ventral prostatic lobes. BDNF immunoreactivity also increased in the nerves. ELISA and reverse transcription/real-time polymerase chain reaction confirmed the findings of the immunohistochemical study. In the accessory glands, castration induced an increase of both BDNF tissue concentration and mRNA expression. These results suggest that BDNF is expressed in the internal male genital organs of the rat and that its expression is downregulated by androgen hormones. We hypothesize that the observed BDNF increases are related to the castration-induced regression of the sympathetic nerves.