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 subunitspecific oligonucleotide probes. The ∈1 subunit mRNA was observed in various brainstem nuclei. On the other hand, the ∈2 and ∈3 subunit mRNAs were restricted to particular nuclei, and the ∈4 subunit mRNA was detected in several nuclei at very low levels. The dorsal cochlear nucleus exhibited differential expressions of the ∈ subunit mRNAs in distinct neuron types: the ∈2 subunit mRNAin the pyramidal cells, the ∈3 subunit mRNA in the granule cells, and the ∈1 subunit mRNA in other neurons. In the vestibular nuclei, the medial nucleus expressed the ∈1, ∈3, and ∈4 subunit mRNAs, whereas the lateral and superior nuclei expressed the ∈1 subunit mRNA. Such region-specific expressions were also discerned in the central gray, the superior and inferior colliculi, the medical 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 ∈ subunit mRNAs, intense signals for the ζ1 subunit mRNA were distributed throughout the brainstem. These findings suggest that anatomical organization of the ∈ subunits is heterogeneous in various regions of the brainstem, which would give rise to functional diversity of the NMDA receptor channel in these regions. © 1994 Wiey-Liss, Inc.