The alpha2 subunit of the glycine receptor is expressed transiently in the rat brain during early development suggesting that this subunit may be replaced by the alpha1 subunit in the adult brain. The expression of glycine receptor alpha2 subunit mRNA was investigated in the 7-day-old rat brain by in situ hybridization histochemistry using oligonucleotide probes specific for this subunit. Neurons expressing alpha2 subunit mRNA were found to be widely and abundantly distributed throughout brain. We compared the distribution of neurons expressing alpha2 subunit mRNA with that of neurons expressing alpha1 or beta subunit mRNA. In the lower brainstem, the location of the neurons expressing alpha2 subunit mRNA was very similar to that of the neurons with alpha1 or beta subunit mRNA. Neurons expressing beta subunit mRNA were widespread and numerous in the forebrain, where neurons with alpha1 subunit mRNA were uncommon. The locations of the neurons labeled by the alpha2 probe were very similar to those of the cells labeled by the beta probe. These findings suggest that the alpha2 subunit is not only expressed by immature neurons containing the alpha1 subunit, but is also common to most immature neurons having the glycine receptor. However, it should be noted that several neurons contained beta and/or alpha1 subunit mRNA but lacked alpha2 subunit mRNA, suggesting that the glycine receptor is heterogeneous in its composition during brain development.