The calyx of Held serves as a model for synaptic transmission in the mammalian central nervous system. While offering unique access to the biophysics of presynaptic function, studies addressing the molecular mechanisms of neurotransmitter exocytosis in this model have been mainly limited to pharmacological interventions. To overcome this experimental limitation we used stereotaxic delivery of viral gene shuttles to rapidly and selectively manipulate protein composition in the calyx terminal in vivo. Sindbis or Semliki Forest viruses encoding enhanced green fluorescent protein (EGFP) were injected into the ventral cochlear nucleus (VCN) of rats (postnatal days 7-21) and yielded bright fluorescence in cells of the VCN, including globular bushy cells with their axon and calyx terminal. Fluorescence imaging and three dimensional reconstructions visualized developmental changes in calyx morphology. Small cytoplasmic and synaptic vesicle proteins were successfully overexpressed in the calyx. We extended two-photon microscopy to obtain simultaneous fluorescence and infrared scanning gradient contrast images, allowing for efficient patch-clamp recordings from EGFP-labelled calyces in acute brain slices (postnatal days 9-14). Recordings of spontaneous miniature excitatory postsynaptic currents and short-term depression in synapses overexpressing EGFP or synaptophysin-EGFP revealed normal synaptic function. Thus, Sindbis and Semliki Forest virus-directed overexpression of proteins in the calyx of Held provides a new avenue for molecular structure-function studies of mammalian central synapses.