The neurotrophin brain-derived neurotrophic factor (BDNF) is considered to be a key factor for neuronal survival, differentiation and plasticity. According to a proposed hypothetical model BDNF expression might play a central role in the pathogenesis of depression. The BDNF gene is rather complex in its structure and it can express four different mRNA isoforms by alternative splicing, each producing the same protein. This might reflect fine tuning of gene regulation by different signalling networks. Since the BDNF gene has been reported to be upregulated by antidepressants, the expression of the four BDNF mRNA isoforms was measured by real-time quantitative RT-PCR in rat hippocampi after chronic and acute treatment with the antidepressant drug fluoxetine and GR205171, a selective NK-1 receptor antagonist with anxiolytic-like properties. The aim of this study was to test the hypothesis of differential regulation of the mRNA isoforms by those compounds. Our results indicate that the expression of BDNF mRNA isoforms is not affected by chronic or acute treatment with fluoxetine or GR205171.