In adult spinal neurons inhibitory glycine receptors (GlyR) are localized at postsynaptic membrane specializations underlying glycinergic nerve terminals. The peripheral membrane protein gephyrin has been shown to be essential for the formation of postsynaptic GlyR clusters. Here, we coexpressed GlyR polypeptides and gephyrin in 293 cells and observed rerouting of hetero-oligomeric GlyR and its beta, but not of alpha subunits to intracellular gephyrin aggregates. A GlyR chimeric alpha 1/beta protein was also accumulated at these gephyrin aggregates, indicating that colocalization with gephyrin depends on cytoplasmic domains of the beta subunit. gamma-Aminobutyric acid type-A receptor (GABAAR) subunits were not targeted to intracellular gephyrin aggregates with the exception of the GABAAR beta 3 subunit, which partially colocalized with gephyrin. These data show that gephyrin alters the subcellular localization of the GlyR beta and, to some extent, GABAAR beta 3 subunits. Thus, gephyrin-binding subunits might target hetero-oligomeric ion channels to a gephyrin matrix underlying the differentiating postsynaptic membrane.