We hypothesized that estradiol levels are higher in prepubertal girls than in prepubertal boys and that this greater secretion of estradiol might drive the more rapid epiphyseal development and earlier puberty in girls. Since previous estradiol assays have lacked adequate sensitivity to test the hypothesis of higher estradiol levels in girls, we developed a new ultrasensitive assay to measure estrogen levels. The assay uses a strain of Saccharomyces cerevisiae genetically engineered for extreme sensitivity to estrogen. Yeast were transformed with plasmids encoding the human estrogen receptor and an estrogen-responsive promoter fused to the structural gene for f-galactosidase. Ether extracts of 0.8 ml of serum were incubated with yeast for 8 h and the 38-galactosidase response was used to determine estrogen bioactivity relative to estradiol standards prepared in charcoalstripped plasma. The assay was highly specific for estradiol with < 3 % cross-reactivity with estrone, estriol, or estradiol metabolites. The detection limit was < 0.02 pg/ml estradiol equivalents (100-fold lower than existing assays). Using this assay, we measured estrogen levels in 23 prepubertal boys (9.4±2.0 yr) and 21 prepubertal girls (7.7+1.9 [SD] yr). The estrogen level in girls, 0.6+0.6 pg/ml estradiol equivalents, was significantly greater than the level in boys, 0.08+0.2 pg/ml estradiol equivalents (P < 0.05). We conclude that the ultrasensitive recombinant cell bioassay for estrogen is approximately 100-fold more sensitive than previous estradiol assays, that estrogen levels are much lower prepubertally, in both sexes, than reported previously, and that prepubertal girls have 8-fold higher estrogen levels than prepubertal boys. (J. Clin. Invest. 1994Invest. . 94:2475Invest. -2480