In the present study, the distribution of GABA(A)-receptor alpha(1)-, alpha(2)-, alpha(3)-, alpha(5)-, beta(2,3)- and gamma(2)-subunits were localized immunohistochemically with subunit specific antibodies in the rat circadian timing system (CTS), The areas examined include the principal circadian pacemaker, the suprachiasmatic nucleus (SCN), and areas that receive important SCN input including the intergeniculate leaflet (IGL), subparaventricular zone (SPVZ), paraventricular hypothalamic nucleus (PVH)I the retrochiasmatic area (RCh) and the paraventricular nucleus of the thalamus (PVT). The SCN has an unusual pattern with immunoreactivity for the alpha(2)-, alpha(3)-, alpha(5)- and gamma(2)-subunits but not for the commonly expressed alpha(1)- and beta(2,3)-subunits. In all of the areas receiving SCN efferent input (SPVZ, PVH, RCh, PVT and IGL), staining is present either for all six subunits or for the three common subunits, alpha(1)-, beta(2,3)- and beta(2). There is some evidence for a differential distribution of subunits at the cellular level. The alpha(2)- and beta(2,3)-subunits are predominantly expressed in neuropil, the alpha(3)-, alpha(5)- and gamma(2)-subunits are predominantly expressed over perikarya and the alpha(1)-subunit is expressed over both neuropil and perikarya in the areas in which subunit immunoreactivity is found. The demonstration of this regional and cellular expression of GABA(A)-receptor subunits should contribute to our understanding of GABAergic neurotransmission in the CTS.