Pyramidal cells of CA3 area receive glutamatergic signals from the mossy fibers (MFs), perforant path and collaterals of other pyramidal cells, as well as GABAergic inputs from interneurons. In hippocampal slices, an extracellular stimulation electrode is often used to activate the MFs, with the disadvantage of possibly activating fibers other than MFs. We set-up a preparation that allows the analysis of the glutamatergic input from identified, giant MF boutons as well as of GABAergic inputs from boutons of interneurons on single CA3 pyramidal cells. Mossy fiber boutons were labeled by exposing hippocampal slices to a zinc-reactive fluorescent dye, or by injecting a fluorescent dye in the granule cell layer and allowing its transport along the MFs to their terminals in CA3 area. After conducting an enzyme-free, mechanical dissociation of CA3 area, we obtained pyramidal cells containing fluorescent, giant MF boutons attached to their apical dendrites, as well as boutons of interneuronal origin. Whole cell recordings were then performed, whereby synaptic responses could be evoked by selective stimulation of the identified boutons. The synaptic currents evoked by stimulation of MF boutons, unlike those evoked by stimulation of interneuronal boutons, underwent strong frequency potentiation and were depressed by activation of metabotropic glutamate receptors, which are characteristics of transmission of MF origin. Combination of fluorophores can be used to label different tracts/boutons allowing the study of the different characteristics of neurotransmitter release from a variety of sources on single target cells.