These studies represent the first biochemical characterization and purification of nuclear type II binding sites from the rat uterus. Uterine nuclei from estradiol-implanted rats were digested with DNA'se and RNA'se, washed with Na deoxycholate-Tween 40 and extracted with 0.4 M ammonium sulfate (AmSO4). Nuclear type II sites in the AmSO4 extract eluted as a single peak during DEAE ion exchange chromatography, HPLC (Waters DEAE 5PW column) and Sephadex G-100 chromatography with a molecular weight of approximately 37K. DEAE and quercetin-sepharose affinity chromatography resulted in significant purification (greater than 800-fold) of nuclear type II sites with a 49% yield. Type II sites were not recognized by rat ER antibodies (Abbot ER-EIA kit) which immunoadsorbed ER from these preparations. These biochemical and immunological studies suggest that the ER and type II sites are likely to be different proteins.