AbstractGephyrin is a multifunctional protein responsible for the clustering of glycine receptors (GlyR) and γ‐aminobutyric acid type A receptors (GABAAR). GlyR and GABAAR are heteropentameric chloride ion channels that facilitate fast‐response, inhibitory neurotransmission in the mammalian brain and spinal cord. We investigated the immunohistochemical distribution of gephyrin and the major GABAAR and GlyR subunits in the human light microscopically in the rostral and caudal one‐thirds of the pons, in the middle and caudal one‐thirds of the medulla oblongata, and in the first cervical segment of the spinal cord. The results demonstrate a widespread pattern of immunoreactivity for GlyR and GABAAR subunits throughout these regions, including the spinal trigeminal nucleus, abducens nucleus, facial nucleus, pontine reticular formation, dorsal motor nucleus of the vagus nerve, hypoglossal nucleus, lateral cuneate nucleus, and nucleus of the solitary tract. The GABAAR α1and GlyR α1and β subunits show high levels of immunoreactivity in these nuclei. The GABAAR subunits α2, α3, β2,3, and γ2present weaker levels of immunoreactivity. Exceptions are intense levels of GABAAR α2subunit immunoreactivity in the inferior olivary complex and high levels of GABAAR α3subunit immunoreactivity in the locus coeruleus and raphe nuclei. Gephyrin immunoreactivity is highest in the first segment of the cervical spinal cord and hypoglossal nucleus. Our results suggest that a variety of different inhibitory receptor subtypes is responsible for inhibitory functions in the human brainstem and cervical spinal cord and that gephyrin functions as a clustering molecule for major subtypes of these inhibitory neurotransmitter receptors. J. Comp. Neurol. 518:305–328, 2010. © 2009 Wiley‐Liss, Inc.