The distribution of five NMDA receptor channel subunit mRNAs in the mouse brainstem at postnatal day 21 was semiquantitatively examined by in situ hybridization with subunit-specific oligonucleotide probes. The epsilon 1 subunit mRNA was observed in various brainstem nuclei. On the other hand, the epsilon 2 and epsilon 3 subunit mRNAs were restricted to particular nuclei, and the epsilon 4 subunit mRNA was detected in several nuclei at very low levels. The dorsal cochlear nucleus exhibited differential expression of the epsilon subunit mRNAs in distinct neuron types: the epsilon 2 subunit mRNA in the pyramidal cells, the epsilon 3 subunit mRNA in the granule cells, and the epsilon 1 subunit mRNA in other neurons. In the vestibular nuclei, the medial nucleus expressed the epsilon 1, epsilon 3, and epsilon 4 subunit mRNAs, whereas the lateral and superior nuclei expressed the epsilon 1 subunit mRNA. Such region-specific expressions were also discerned in the central gray, the superior and inferior colliculi, the medial accessory oculomotor nucleus, the locus ceruleus, the parabrachial nucleus, nucleus of the solitary tract, the caudal subnucleus of the trigeminal spinal tract nucleus, and the inferior olive. In contrast to the differential distributions of the four epsilon subunit mRNAs, intense signals for the zeta 1 subunit mRNA were distributed throughout the brainstem. These findings suggest that anatomical organization of the epsilon subunits is heterogeneous in various regions of the brainstem, which would give rise to functional diversity of the NMDA receptor channel in these regions.