Androgen receptor (AR) gene expression in the central nervous system (CNS) and peripheral tissues of male rats was examined using cDNA probes to measure AR mRNA by RNA (Northern) blot analysis and by in situ hybridization. Using a probe from the 5′ untranslated region of the rat cDNA (AR-1), a single mRNA species of approximately 11 kb was seen in Northern blots of poly(A)+ RNA from reproductive tissues, kidney, liver, and muscle. Using a probe from the 5′ end of the coding region (AR-2), in addition to the 11-kb band, a novel transcript was seen in whole brain at about 9.3 kb. In poly(A)+ RNA from dissected brain regions, the 9.3-kb transcript was predominant in the cortex, cerebellum, and brain stem, while in the hippocampus, both transcripts were expressed to a similar degree. AR mRNA levels increased two- to threefold in the prostate on Days 1 and 3 following castration but no significant change was seen in either CNS transcript in whole brain or cortex. Specific in situ hybridization of an 35S-labeled AR-2 riboprobe was observed in brain regions known to bind radiolabeled androgens. We conclude that two AR RNA species exist in the adult male rat which differ in their 5′ untranslated region and that the relative proportion of the two species varies between brain regions. In contrast to observations in the prostate, AR gene expression in the cerebral cortex is not regulated in the short term by androgen withdrawal.