Recent studies have identified a new family of gap junction-forming proteins in vertebrates, called pannexins. Although their function in vivo is still not known, studies in Xenopus oocytes have indicated that pannexin1 (Px1) and pannexin2 (Px2) can form functional gap junction channels and can contribute to functional hemichannels. In this study, we have utilized a combination of radioactive and non-radioactive in situ hybridization experiments to characterize the expression pattern of the two pannexin genes during development and maturation of the rat brain. Expression analysis revealed a widespread and similar mRNA distribution for both genes, but indicated that Px1 and Px2 are inversely regulated during the development of the rat brain. Px1 is expressed at a high level in the embryonic and young postnatal brain and declines considerably in the adult, whereas Px2 mRNA is low in the prenatal brain but increases substantially during subsequent postnatal development. Immunohistochemical studies using different antibodies confirm the neuronal origin of pannexin-expressing cells and ascertain the presence of both pannexins in the majority of pyramidal cells and in GABAergic interneurons. The abundant presence of both pannexins in most neurons suggests that they may play a role in intercellular communication in many neuronal circuits. Furthermore, the temporal difference in the expression of the two genes indicates that the relative contribution of the two pannexins in immature and mature neuronal circuits may vary.