Neurotrophins enhance and maintain some neuronal phenotypes and suppress others by influencing the expression of neuropeptides and calcium binding proteins, thereby affecting many different physiological functions of the brain. Brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT3) show different effects on neuronal phenotypes despite largely overlapping expression of their respective receptors, TrkB and TrkC. Using BDNF null mutant (BDNF-/-) mice and mice where the protein coding DNA sequence of BDNF has been replaced by NT3 (BDNFNT3/NT3 mice), we have analysed the roles of BDNF and NT3 in controlling neuropeptide and calcium binding protein expression in the brain. Our results show that NT3 expressed emporally and spatially in the place of BDNF is sufficient in some neuronal populations to compensate for the loss of BDNF.