Estrogen regulates thymic development and immune function. Despite the critical role of estrogens in inducing thymic involution and modulating immune responses, the mechanism of this effect is unclear. Similarly, humans and animals are exposed to increasing amounts of the estrogenic soy isoflavone genistein in the diet, but whether genistein can induce immune changes has not been definitively established. We reported previously that genistein induces thymic atrophy in mice, and decreases both humoral and cell-mediated immunity. These thymic effects of genistein occur via estrogen receptor (ER)-mediated and non-ER-mediated pathways. Genistein injections produced the most pronounced effects, but dietary administration to mice that produced serum genistein concentrations similar to those reported in human infants consuming soy formula also had demonstrable effects. Microarray analysis of the effects of estradiol and genistein on neonatal thymus indicated that estradiol affected genes involved in transcription, apoptosis, cell cycle, and thymic development and function; genistein had similar effects on many estradiol target genes, but also had unique actions not replicated by estradiol. Despite extensive work showing inhibitory effects of genistein on immunity, other rodent studies reported that genistein or other phytoestrogens stimulate various aspects of immune function. Although the present data strongly indicate that genistein can regulate immune function, possibly at physiologic concentrations, further work is required to definitively establish overall thymic and immune effects of genistein and soy, which may vary with age, species, and specific end point.