Dmrt1bY (aka dmy) has been identified as the master male sex-determining gene of medaka by positional cloning and genetic evidence. How this gene on the molecular level determines the differentiation of the gonad primordium towards a testis, however, is unknown. To better understand the roles of dmrt1bY and its autosomal counterpart dmrt1a in the process of sex determination, a detailed expression analysis by quantitative real-time RT-PCR was performed showing non-organ-specific expression of dmrt1bY during embryogenesis and low expression in adult testes. Surprisingly a high expression of dmrt1bY was noted in the spleen of males. Dmrt1a is exclusively expressed in adult testes, 50 times higher than dmrt1bY. Dmrt1bY mRNA and protein have short half-lives and the GFP fusion protein products of both dmrt1 genes are localized to the nucleus. These features are consistent with the suggestion that Dmrt1 proteins might function as DNA-binding transcription factors.