Regional variation in the alternative splice forms of the NMDAR1 subunit mRNA was investigated by in situ hybridization in the adult rat brain, using radiolabelled splice-specific oligonucleotide probes. Each splice variant was detected in an individual distribution. The NMDAR1-a and NMDAR1-2 forms were widely and abundantly distributed throughout the brain, except for the inferior colliculus. The NMDAR1-b and NMDAR1-4 variants were located in similar patterns in fewer areas (e.g. parietal cortex, hippocampus CA3, thalamus, inferior colliculus, cerebellar granule cells). In contrast, the NMDAR1-1 forms were distributed in a pattern approximately complementary in the forebrain to that of NMDAR1-4 (weakly expressed in thalamus and inferior colliculus). The NMDAR1-3 variants were not abundant in any structure. Considerable overlap of the in situ hybridization images was noted, so all eight splice combinations are possible in heterogenous distributions. Correlation of the distribution of NMDAR1 mRNA splice forms with functional analyses of heteromeric recombinant receptors will be necessary to ascertain if alternative splicing of the NMDAR1 subunit can account for some of the known heterogeneity of endogenous NMDA receptors.