The effects of estradiol, nafoxidine, and clomiphene on uterine histology and nuclear type I and type II estrogen binding sites were examined 96 h following administration of these compounds to mature-ovariectomized rats by beeswax implant. Histological examination revealed that estradiol treatment resulted in dramatic stimulation of the luminal epithelium, stroma, and myometrium. Clomiphene and nafoxidine treatment resulted in intense stimulation of the luminal and glandular epithelium; however, these compounds were only partial agonists in the stroma and myometrium. Increases in uterine wet weight and DNA content correlated with this differential cell stimulation. To examine the biochemical basis for this differential cellular response, nuclear levels of type I and type II estrogen binding sites were measured in isolated uterine luminal epithelium, stroma, and myometrium. Estradiol, nafoxidine, or clomiphene treatment caused the accumulation of type I sites in the nuclei of the luminal epithelial, stromal, and myometrial cells. In addition, estradiol stimulation was associated with dramatic increases in nuclear levels of type II sites in the luminal epithelium (13-fold), stroma (10-fold), and myometrium (30-fold). Likewise, the agonistic properties of nafoxidine and clomiphene correlated with a two- to eightfold increase in nuclear type II sites in the luminal epithelium and stroma. In contrast, these drugs failed to stimulate significant increases in nuclear type II sites in the myometrium. These results demonstrate that estradiol, nafoxidine, and clomiphene differentially stimulate the uterine luminal epithelium, stroma, and myometrium. In addition, the high correlation between nuclear levels of type II sites and estrogenic stimulation of target cell growth, particularly in the uterine stroma and myometrium, suggests that these sites are a good biochemical endpoint for assessing the estrogenic or “antiestrogenic” properties of various compounds. These procedures are extremely useful when nuclear occupancy by the estrogen receptor does not accurately reflect the level of estrogenic stimulation, as is the case following the administration of triphenylethylene derivatives.