BDNF and NT-3 can modulate the development and plasticity of central synaptic transmission. Although the expression of NT-3 and BDNF in the rodent hippocampus coincides during perinatal development, little is known about possible functional interactions between both neurotrophins in synaptic development. Here, we have investigated the effects of combined long-term application of NT-3 and BDNF on excitatory glutamatergic (mEPSC) and inhibitory GABAergic miniature synaptic currents (mIPSC) in cultured embryonic hippocampal neurons. Our results show that the BDNF-induced twofold increase in mEPSC frequency is abolished by pre-treatment with NT-3. In addition, the NT-3-induced twofold downregulation of mIPSC frequency is reversed by BDNF. Finally, the BDNF-induced increase in c-fos expression is reduced by 50% after pre-treatment with NT-3. In summary, these data suggest an NT-3 controlled modulation of BDNF signalling in differentiating hippocampal neurons.