Neurotrophins modulate synaptic transmission and plasticity in the adult brain. We here show a novel feature of this synaptic modulation, i.e. that two populations of excitatory synaptic connections to granule cells in the dentate gyrus, lateral perforant path (LPP) and medial perforant path (MPP), are differentially influenced by the neurotrophins BDNF and NT-3. Using field recordings and whole-cell patch-clamp recordings in hippocampal slices, we found that paired-pulse (PP) depression at MPP-granule cell synapses was impaired in BDNF knock-out (+/-) mice, but PP facilitation at LPP synapses to the same cells was not impaired. In accordance, scavenging of endogenous BDNF with TrkB-IgG fusion protein also impaired PP depression at MPP-granule cell synapses, but not PP facilitation at LPP-granule cell synapses. Conversely, in NT-3+/- mice, PP facilitation was impaired at LPP-granule cell synapses whilst PP depression at MPP-granule cell synapses was unaffected. These deficits could be reversed by application of exogenous neurotrophins in an afferent-specific manner. Our data suggest that BDNF and NT-3 differentially regulate the synaptic impact of different afferent inputs onto single target neurons in the CNS.