We analyzed the distribution of the receptor-anchoring protein gephyrin in the normal and deafferented rat dentate gyrus to investigate whether the expression of this postsynaptic protein is altered in response to the formation of new synaptic contacts. Confocal microscopy and digital image analysis revealed that in normal dentate gyrus immunolabeling was most prominent in the outer molecular layer and decreased successively in the direction of the granule cell layer. Simultaneous immunolabeling for gephyrin and cell-specific markers showed that granule cells and parvalbumin-positive interneurons express gephyrin. Large, intensely stained, gephyrin-positive clusters were distributed along distinct dendrites, and most of them were positive for parvalbumin. Calbindin-immunostained dendrites were associated with smaller, gephyrin-positive clusters. Lesion of the medial entorhinal cortex leads to deafferentiation of the middle molecular layer which resulted in an increased gephyrin immunoreactivity. These changes were due to a significantly increased concentration of the very small gephyrin-positive clusters. Parvalbumin-positive dendrites did not display any increase in co-localizing gephyrin-positive structures. The altered immunolabeling pattern persisted until 12 weeks after lesion, a time when the process of synaptic reorganization is complete. Our findings suggest that synaptogenesis following deafferentiation results in a cell-specific redistribution of gephyrin immunoreactivity at specific inhibitory synapses.