Reverse transcription-polymerase chain reaction (RT-PCR)-Southern blotting was employed for biochemical detection and measurement of the estrogen receptor messenger ribonucleic acid (ERmRNA) in various parts of the Wistar strain female rat brain. Total RNA extracted from the tissues was subjected to RT-PCR using the primer set which flanked the part(287bp) of the estrogen binding domain-corresponding region of the rat ERcDNA. It was confirmed that the RT-PCR product corresponded to the part of the ERcDNA by direct nucleotide sequencing of the product. Moreover, the level of ERmRNA could be determined by Southern blotting which was highly sensitive and produced quantitative results. The RT-PCR product of about 290 bp, corresponding in length to the distance between two primers, was generated from RNA of all the tissues examined. The levels of the product were as follows; anterior hypophysis greater than hypothalamus and preoptic area, amygdala much greater than cerebral cortex, cerebellum. These results indicate that ERmRNA is widely distributed in the whole brain, implying some physiological action of estrogen on target and 'non-target' brain regions.