Being utilized by over 40% of the amacrine cells, glycine is considered to be a major inhibitory neurotransmitter in the retinas of all vertebrate species examined. Localization of gephyrin, which is a 93-kD peripheral membrane glycine receptor-associated anchoring protein, has been used in several studies to identify the sites of glycinergic interactions in the retina and other regions of the central nervous system. Recent studies have shown that gephyrin colocalizes with GABA(A) receptors which, like those for glycine, are also inhibitory amino acid receptors usually associated with a chloride channel. In the present study, we have used two antibodies which recognize either gephyrin (mAb7a), or the alpha and beta subunits of the glycine receptor (mAb4a) in order to determine to what extent gephyrin is associated with glycine receptors in the mammalian retina. Single-label studies showed extensive punctate staining throughout most of the inner plexiform layer with each antibody. Double labeling showed that nearly 90% of the glycine receptor sites were also immunoreactive for gephyrin. However, nearly 60% of the total punctae immunoreactive for gephyrin were not stained for glycine receptors. This distinction was most pronounced in the most proximal inner plexiform layer where only 24% of the gephyrin-immunoreactive sites were glycine receptor positive. This study suggests that although most glycine receptors in the rabbit retina colocalize with the anchoring protein gephyrin, a significant proportion of the gephyrin-labeled sites are not associated with glycine receptors. In light of studies showing gephyrin association with GABA(A) receptor subunits, the localization of gephyrin may be indicative of chloride-mediated inhibitory amino acid transmission in general and not solely that of glycinergic. Given several studies which show that bipolar cells express glycine receptors and respond to glycine but do not express gephyrin, the 10% of glycine receptors not colocalized with gephyrin shown in the present study may represent a subtype of glycine receptors found on bipolar cells which do not require gephyrin for the functional clustering of receptor subunits.