Gene profiling of Japanese medaka (Oryzias latipes) was performed using an oligonucleotide DNA microarray representing 22,587 TIGR O. latipes gene indices (OLGIs). The average correlation coefficients for gene expression between individual mature fish were high (>0.95) for both female and male, indicating that the physiological status of medaka is highly reproducible under prescribed growth conditions. Of the 22,587 OLGIs, 2575 showed significant differences in expression between female and male. Exposure to 17beta-estradiol (E2) revealed 381 E2-responsive OLGIs in male medaka. Feminization and male-dysfunction factors of the E2-treated males calculated using the combination of Pearson correlation coefficient and Euclidean distances indicate that E2 treatment "weakly feminized" male medaka, while male physiological functions were not significantly disrupted. This study demonstrates the possibility of using medaka microarrays to estimate the overall effects of hormonally active chemicals.