Use of soy-based infant formulas and soy͞isoflavone supplements has aroused concern because of potential estrogenic effects of the soy isoflavones genistein and daidzein. Here we show that s.c. genistein injections in ovariectomized adult mice produced doseresponsive decreases in thymic weight of up to 80%. Genistein's thymic effects occurred through both estrogen receptor (ER) and non-ER-mediated mechanisms, as the genistein effects on thymus were only partially blocked by the ER antagonist ICI 182,780. Genistein decreased thymocyte numbers up to 86% and doubled apoptosis, indicating that the mechanism of the genistein effect on loss of thymocytes is caused in part by increased apoptosis. Genistein injection caused decreases in relative percentages of thymic CD4 ؉ CD8 ؊ and double-positive CD4 ؉ CD8 ؉ thymocytes, providing evidence that genistein may affect early thymocyte maturation and the maturation of the CD4 ؉ CD8 ؊ helper T cell lineage. Decreases in the relative percentages of CD4 ؉ CD8 ؊ thymocytes were accompanied by decreases in relative percentages of splenic CD4 ؉ CD8 ؊ cells and a systemic lymphocytopenia. In addition, genistein produced suppression of humoral immunity. Genistein injected at 8 mg͞kg per day produced serum genistein levels comparable to those reported in soy-fed human infants, and this dose caused significant thymic and immune changes in mice. Critically, dietary genistein at concentrations that produced serum genistein levels substantially less than those in soy-fed infants produced marked thymic atrophy. These results raise the possibility that serum genistein concentrations found in soy-fed infants may be capable of producing thymic and immune abnormalities, as suggested by previous reports of immune impairments in soy-fed human infants. S oy-based formula for human infant nutrition is widely used, with approximately 25% of formula-fed infants in the U.S. consuming soy-based formula (1). This number represents 15% of all infants in the U.S., or about 750,000 infants͞year (1, 2). Infants consuming soy formula are exposed to high levels of genistein and daidzein, estrogenic isoflavones present in soybeans and soy products. On average, infants fed soy-based formula consume 6.0-11.9 mg of isoflavones͞kg per day (3, 4), an order of magnitude greater than adults eating high-soy diets. Total plasma levels of isoflavones and genistein in soy-fed infants range from 2.0 to 6.6 and 1.5 to 4.4 mol͞liter, respectively (3), 10-fold greater than levels in Japanese adults whose diets have historically included soy, and 200-fold greater than plasma levels in infants fed cow's milk formula or human breast milk (3, 5). Levels of the free genistein aglycone as a percent of total genistein are higher in rat pups than in adults (6), but have not been measured in human infants. If a similar phenomenon occurs in humans, relative levels of the biologically active free aglycones may be even greater than the 10-fold difference documented in total (free ϩ conjugated) serum isoflavone and genistein levels in...