Gene expression within the central nervous system is regulated by complex interactions of DNA-binding proteins, among which are the POU domain-containing proteins, which are distantly related to homeobox proteins. These POU domain-containing proteins have been implicated in control of transcription and replication within the central nervous system. We used degenerate primers with the PCR to isolate another POU domain-containing cDNA, RHS2, from hypothalamic RNA. Isolation of a putative full-length cDNA was accomplished by using serial dilutions of a hypothalamic cDNA library grown on solid medium. This member of the class III POU family is expressed in rats from embryonic day 11.5 into adulthood, being especially prominent in the brain. We performed double-labeling hybridization histochemistry and determined that RHS2 is coexpressed with a variety of neuropeptides in medium-sized neurons in the caudate putamen and with dynorphin in the paraventricular and supraoptic nuclei of the hypothalamus. Expression of RHS2 in the caudate putamen was increased by elimination of its nigrostriatal dopaminergic innervation.