We used a multiprobe oligonucleotide solution hybridization technique to examine the regulation of gene expression of NR1, NR2A, NR2B, NR2C, and NR2D in the left rat brain after treatment with the optical isomers of flupenthixol. At a dose of 0.2 mg/kg per day over 1, 2, 4, 8, 12, and 24 weeks, we found that both isomers downregulated the expression of NR1 mRNA in most regions of the brain. NR2A, NR2B, and NR2C showed significantly decreased expression from 12 to 24 weeks of treatment, but after 2 weeks NR2B, NR2C, and NR2D expression had increased in several brain regions. NR1 immunoreactivity in the right brain after 4 and 24 weeks of drug treatment was also examined with Western blotting. Both cis- and transflupenthixol significantly decreased NR1 immunoreactivity in the right cerebellum after 24 weeks of treatment. Expression of the GluR1–7, KA1, and KA2 glutamate receptor mRNAs in the left rat brain were also studied. Neither cis- nor transflupenthixol was found to alter the gene expression of any of the nine non–NMDA glutamate receptor subunits. On the other hand, we found a nearly twofold increase in gene expression of the dopamine D2 receptor in specific brain regions.