The molecular mechanisms regulating sexual differentiation of the brain are largely unknown, although progress is being made, particularly in some mammalian systems. To uncover more of the key factors, a screen was conducted for genes involved in sexually dimorphic development of the neural song system in zebra finches. cDNA microarrays were initially used to compare gene expression in the telencephalons of hatchling and juvenile males and females. Then, real-time quantitative polymerase chain reaction (PCR) was employed to confirm sex differences, and the brain regions expressing the cDNAs of interest were localized using in situ hybridization. Several genes, including those likely to encode two ribosomal proteins (RPL17 and RPL37), SCAMP1, ZNF216, and a COBW-domain containing protein, showed enhanced expression in the telencephalon of males compared to females. In several cases, expression in the song control nuclei specifically was detected only in males. Interestingly, the sequences of some of these cDNAs shared substantial homology with regions of the chicken Z chromosome (male birds are ZZ, females ZW). Thus, we have identified genes likely to be involved in masculinization of the structure and/or function of the song circuit, some of which could be initial triggers for the sexual differentiation process.