Estrogen administration to mature-ovariectomized rats causes the activation or stimulation of secondary nuclear estrogen-binding sites (type II) in the uterus which can interfere with estrogen receptor (type I) measurement. Earlier reports from our laboratory have shown that quantitation of type I sites in the presence of the type II site is very difficult and can only be achieved by graphic analysis of saturation curves which employ a wide range (0.4-40 NM) of [3H]estradiol concentrations in nuclear exchange assay. The studies presented in this manuscript describe simple methods which can be used to separately quantitate both nuclear estrogen-binding sites using a single concentration of [3H]estradiol. Since the nuclear type II site does not bind [3H]estradiol in the presence of reducing agent, type I sites can be easily quantitated by incubating nuclei (37 C for 30 min) in Tris-EDTA buffer containing 0.1-1.00 mM dithiothreitol using a single saturating concentration of [3H]estradiol. Conversely, a single concentration of [3H]estradiol (40-80 nM) can be used to quantitate the nuclear type II site by incubating nuclei in Tris-EDTA buffer under conditions (4 C for 60 min) which do not measure occupied nuclear estrogen receptor. Therefore, by using the appropriate buffer system, type I and type II sites can be easily separated in mixed binding systems. In addition, we also demonstrate that Nafoxidine does not bind to the nuclear type II site. Therefore, it can be used as a competitive inhibitor of [3H]estradiol binding to type I sites and permit the measurement of type II sites without interference from type I sites. These techniques should be applicable to autoradiographic or fluorescence studies which cannot discriminate between steroid binding to these two classes of nuclear estrogen-binding sites.