Gephyrin is a scaffold protein essential for stabilizing glycine and GABA A receptors at inhibitory synapses. Here, recombinant intrabodies against gephyrin (scFv-gephyrin) were used to assess whether this protein exerts a transynaptic action on GABA and glutamate release. Pair recordings from interconnected hippocampal cells in culture revealed a reduced probability of GABA release in scFv-gephyrin-transfected neurons compared with controls. This effect was associated with a significant decrease in VGAT, the vesicular GABA transporter, and in neuroligin 2 (NLG2), a protein that, interacting with neurexins, ensures the cross-talk between the post-and presynaptic sites. Interestingly, hampering gephyrin function also produced a significant reduction in VGLUT, the vesicular glutamate transporter, an effect accompanied by a significant decrease in frequency of miniature excitatory postsynaptic currents. Overexpressing NLG2 in gephyrin-deprived neurons rescued GABAergic but not glutamatergic innervation, suggesting that the observed changes in the latter were not due to a homeostatic compensatory mechanism. Pulldown experiments demonstrated that gephyrin interacts not only with NLG2 but also with NLG1, the isoform enriched at excitatory synapses. These results suggest a key role of gephyrin in regulating transynaptic signaling at both inhibitory and excitatory synapses.Speed and reliability of synaptic transmission are essential for information coding and require the presence of clustered neurotransmitter receptors at the plasma membrane in precise apposition to presynaptic release sites. The postsynaptic organization comprises a large number of proteins that ensure the correct targeting, clustering, and stabilization of neurotransmitter receptors. Among them, the tubulin-binding protein gephyrin plays a crucial role in the functional organization of inhibitory synapses (1). Through its self-oligomerizing properties, gephyrin can form a hexagonal lattice that traps glycine (2) and GABA A receptors in the right place at postsynaptic sites (3, 4) by linking them to the cytoskeleton. Disruption of endogenous gephyrin leads to reduced GABA A receptor clusters (3), an effect that has been shown to be accompanied by a loss of GABAergic innervation (5, 6). This observation suggests the existence of cross-talk between the post-and presynaptic sites. The retrograde control of presynaptic signaling may occur via neuroligins (NLGs), 3 postsynaptic cell adhesion molecules known to transynaptically interact with presynaptic neurexins (7). NLG1 is enriched at glutamatergic synapses (8, 9), whereas NLG2 is preferentially associated with GABAergic connections (10). Overexpression of NLGs has been shown to increase the number of GABAergic and glutamatergic synaptic contacts (11). Interestingly, increasing the expression level of PSD-95, the scaffold molecule that directly binds NLG1, caused an enhancement of the glutamatergic innervation at the expense of the GABAergic one. This effect was accompanied by the recruitment of NLG2 to g...