We used a digoxigenin-UTP-labeled cRNA probe with in situ hybridization and Northern blot analysis to investigate the localization of brain derived neurotrophic factor (BDNF) mRNA and expression of its different transcripts in adult rat hypothalamus. As the BDNF gene is under the control of alternative multiple promoters, which provide tissue-specific gene expression, we studied whether these transcripts were expressed in adult hypothalamus. Our data revealed two novel sources of hypothalamic BDNF mRNA: the supraoptic and periventricular nuclei. In addition, we observed the expression of transcripts from exons, I, II and III as well as the presence of 1.6 and 4.2 kb BDNF mRNAs. Finally, our findings confirmed expression of mRNA encoding neurotrophins receptors in the hypothalamus.