We examined the effects on sexual differentiation of nanoinjecting ethinylestradiol (EE2) into embryos of olvas-GFP/ST-II YI medaka (Oryzias latipes). This strain contains the green fluorescent protein (GFP) gene fused to the regulatory region of the medaka vasa gene, and germ-cell-specific expression of GFP can be visualized in living (transparent) individuals. The number of germ cells in untreated genotypic females (XX) was approximately 10-fold that in untreated genotypic males (XY) at 10 d posthatch (dph). Germ cell proliferation was prevented in XX females that developed from embryos nanoinjected with 0.5, 2.5, or 5.0 ng of EE2. Some 10-dph XY males from embryos injected with 0.5 ng or more of EE2 showed a larger fluorescent area and more germ cells than those of pooled control groups. Males and females from embryos injected with 5.0 ng of EE2 had no significant difference in germ cell number or fluorescent area. Thus, EE2 injection into embryos caused abnormal gonadal development in both sexes. Observations of external secondary sex characteristics and histological examination of adult gonads showed complete sex reversal in some males after 0.5-, 2.5-, and 5.0-ng treatments but no changes in XX females after any treatment. Thus, quantitative bio-imaging can aid in evaluating the effects of endocrine-disrupting chemicals on fish within 10 dph.