Growing evidence suggests that NMDA receptor (NMDAR) dysfunction may be involved in schizophrenia. The NMDAR is a multimeric assembly derived from seven different genes (NR1, NR2A-2D and NR3A-3B). While region-specific changes in the expression of most NMDAR subunits have been reported in schizophrenia, possible abnormalities of NR3A expression have not been investigated. Both electrophysiological and anatomical data in rodents, however, suggest that NR3A subunits could play a role in this disorder. In this study, we measured NR3A transcript levels in the dorsolateral prefrontal cortex (DLPFC) and inferior temporal neocortex in the brains of people with schizophrenia, bipolar disorder, depression, and a comparison group. This transcript was elevated by 32% in schizophrenia relative to controls, but only in the DLPFC and not inferior temporal cortical regions. Interestingly, this effect was restricted to gyral aspects of the DLPFC and did not involve sulcal areas. NR3A mRNA was significantly decreased by 12% in bipolar disorder relative to the comparison group in DLPFC, although there were no gyral versus sulcal differences. As was the case in schizophrenia, no changes in NR3A expression were observed in the inferior temporal cortex in bipolar disorder. These data indicate that the NR3A subunit is abnormally expressed in both schizophrenia and bipolar disorder.