Brain derived neurotrophic factor (BDNF) has been shown to exert multiple actions on neurons. It plays a role in neuronal growth and maintenance and use-dependent plasticity, such as long-term potentiation and learning. This neurotrophin is believed to regulate neuronal plasticity by modifying neuronal excitability and morphology. There is experimental evidence for both an acute and a long-term effect of BDNF on synaptic transmission and structure but the molecular mechanisms underlying these events have not been completely clarified. In order to study the BDNF-induced molecular changes, the set of genes modulated in cultured hippocampal neurons by BDNF treatment was investigated after subchronic treatment with the neurotrophin. Microarray analysis performed with these cells, revealed increased expression of mRNA encoding the neuropeptides neuropeptide Y and somatostatin, and of the secreted peptide VGF (non acronymic), all of which participate in neurotransmission. In addition, the expression of genes apolipoprotein E (ApoE), delta-6 fatty acid desaturase (Fads2) and matrix metalloproteinase 14 (Mmp14), which play a role in neuronal remodelling, was also enhanced. More studies are needed to investigate and confirm the role of these genes in synaptic plasticity, but the results reported in this paper show that microarray analysis of hippocampal cultures can be used to expand our current knowledge of the molecular events triggered by BDNF in the hippocampus.