The molecular nature of tissue-specific gene regulation by androgens has not been well defined, partly as a result of the variable expression and incomplete regulation of currently available gene models. We have therefore aimed to establish more informative models by identifying alternative genes whose expression is tightly and coordinately regulated by androgens. Female C57BL/6 mice were dosed with dihydrotestosterone- or sham-treated for 8 days, after which kidneys were removed and complementary DNA (cDNA) prepared. We then applied the subtractive hybridization techniques of random arbitrarily primed-PCR and PCR-coupled subtractive hybridization method of cDNA representational difference analysis to the isolated cDNA. In addition to well characterized androgen-regulated genes [e.g. KAP (kidney androgen-regulated protein)], we demonstrate the differential expression of six genes previously not known to be under androgen control. RNA levels of SA, Cytochrome P450 4B1, IL-6ST (interleukin-6 signal transducer), OATP (organic anion transporter), and a newly identified gene, MJAM, were up-regulated by androgen, while 16-alpha-hydroxylase was decreased. Expression of these transcripts was inhibited in dihydrotestosterone-treated females by flutamide and in males by castration, confirming their dependence on androgens. Although all the genes demonstrate tissue-specific regulation by androgen, SA showed both kidney specificity and absolute requirement for androgen for its expression. These newly identified androgen-regulated genes will constitute very useful models for studying the nature of tissue-specific gene regulation by androgens.