The effect of partial glycinergic denervation on the cellular distribution of the 93 kDa peripheral polypeptide associated with the glycine receptor was studied at the level of the teleost Mauthner cell, an identified neuron of the goldfish brain (Carassius auratus). Previous studies using monoclonal antibodies raised against purified glycine receptors and immunoperoxidase staining have shown that these proteins are localized in clusters on the entire surface of this neuron. Specifically, the 93 kDa polypeptide was situated only on the cytoplasmic side of the postsynaptic membrane facing active zones. Unilateral electrolytic lesions of the vestibular complex caused the degeneration of some glycinergic afferents to this neuron. When the first signs of this response appeared, 3 d after the surgery, there was also a change in the ultrastructural distribution of the 93 kDa polypeptide in the deafferented cell. The synaptic protein apposed to degenerating axons did not spread onto adjacent extrasynaptic membranes, and it disappeared a few hours after the disruption of its presynaptic element. At the same time, a cytoplasmic immunoreactivity appeared as randomly distributed clusters in the deafferented Mauthner cell; these aggregates, not seen in control preparations, were never found inside membrane-bound organelles. In some preparations these clusters were localized along arrays at a relatively constant distance from the plasma membrane. The intracellular immunoreaction product was found in the soma and the initial part of the dendrites, gradually decreasing in number and intensity toward the extremities of these processes. At later postoperative stages, 10–15 d after surgery, the 93 kDa immunoreactivity remained only at postsynaptic membranes facing intact terminals. Similar alterations following denervation were observed in reticular neurons, at the level at which degenerating presynaptic terminals were also detected. In contrast, continuous 3-d blockade of synaptic transmission by strychnine, an antagonist of the glycine receptor, had no effect on either the distribution of the surface receptor clusters, or the 93 kDa peripheral protein linked to these receptors. Taken together, our results suggest that the ultrastructural distribution of the glycine receptor complex is regulated by “trophic” factors rather than by transmitter-evoked synaptic activity.