The estrogenic isoflavone compound genistein recently has been found in the effluents of sewage treatment plants and pulp mills, and the related compound equol has been detected in the runoff from agricultural fields treated with hog manure. Waterborne exposures of Japanese medaka (Oryzias latipes) to equol from soon after hatch to approximately 100 days posthatch induced gonadal intersex (i.e., testis-ova) in males at incidences of 10 and 87% in equol treatments of 0.4 and 0.8 µg/L, respectively. Exposure to the highest test concentration of genistein, 1,000 µg/L, also caused a low incidence (i.e., 12%) of gonadal intersex in male medaka. The ovaries of female medaka from both equol and genistein treatments showed delayed oocyte maturation, atretic oocytes, an enlarged ovarian lumen, proliferation of somatic stromal tissue, and primordial germ cells; responses were concentration dependent. Alterations to externally visible secondary sex characteristics occurred in medaka exposed to both equol and genistein. In treatments with 1,000 µg/L genistein, 72% of male medaka (as identified by the gonadal phenotype) showed feminized secondary sex characteristics. Gonadal intersex and alterations to secondary sex characteristics have been noted in several fish populations around the world. This laboratory study indicates that isoflavone compounds should be considered candidate estrogenic compounds that may be involved in the alteration of sexual development in feral fish populations.