Recent work from our laboratory has demonstrated that the gap junction proteins connexin26 (Cx26) and connexin32 (Cx32) are expressed in neurons in putative CO2-chemosensitive brainstem regions in both neonatal and adult rats. Whether the recently identified neuron-specific gap junction protein connexin36 (Cx36) is also present in these brainstem regions remains to be determined. Therefore, in the current experiments, immunoblot and immunohistochemical protocols were used to investigate the regional distribution and cellular localization of Cx36 in putative CO2-chemosensitive brainstem regions in both neonatal and adult rats. Immunoblot analyses revealed Cx36 expression in putative CO2-chemosensitive brainstem regions in each of the age groups examined, although both regional and developmental differences in the relative expression levels were detected. Immunohistochemical analyses confirmed Cx36 expression in neurons in each of the putative CO2-chemosensitive brainstem regions and revealed both somal and dendritic labeling patterns. These findings provide additional morphological evidence supporting the potential for gap junctional communication in these regions in both neonatal and adult rats. We propose that the gap junction protein Cx36 also contributes to the neuroanatomical substrate for gap junctional communication, which is hypothesized to play a role in central CO2 chemoreception.