The present study examined the distributions of connexin43 mRNA and connexin32 mRNA in the central nervous system (CNS) of the rat by using in situ hybridization histochemistry. These connexins are the best studied gap junction proteins; connexin32 forms direct cell-cell channels in the liver, as does connexin43 in the heart. There was a differential distribution of cells containing connexin32 mRNA compared with the population of cells which contained connexin43 mRNA, thus implying a regional specificity in the expression of connexins in the CNS. Cells containing connexin43 mRNA were uniformly distributed throughout the gray matter of the neuraxis. Several areas had a higher concentration of cells that express connexin43, such as layer IA of the piriform cortex, supraoptic and paraventricular nuclei of the hypothalamus, anterior cortical amygdaloid nucleus, the reticular part of the substantia nigra, lateral habenula, mesencephalic trigeminal nucleus. Purkinje cell layer of the cerebellum, facial nucleus, prepositus hypoglossal nucleus, and dorsal cochlear nucleus. The pattern of connexin43 hybridization and the morphology of connexin43 mRNA containing cells suggest that this gap junction forming protein is found predominantly in astrocytes. Connexin32 mRNA was detected in discrete cell groups of the gray matter that appeared to be neurons, including cells in layer 2 of the neocortex, layer II of the piriform cortex, pyramidal cell layer of the hippocampus, granule and polymorphic cell layers of the dentate gyrus, islands of Calleja, olfactory tubercle, lateral thalamic nuclei, lateral habenula, and Purkinje cell layer of the cerebellar cortex. A large population of cells in white matter tracts that were labelled with the connexin32 riboprobe appeared to be oligodendrocytes. These studies suggest that neurons and glial cells express connexin32 mRNA, but only astrocytes express connexin43 mRNA. Many of the areas in which connexin mRNAs were demonstrated have electrically coupled cells, morphologically distinct gap junction plaques, and/or have immunocytochemically identifiable connexin proteins. These results indicate that cells with mRNAs coding for intercellular channels have a widespread distribution in the mammalian CNS.