Because endometriosis, a chronic disease affecting 7% to 10% of women, is associated with immunologic aberrations, the authors hypothesize that the presence of specific immune alterations may be diagnostic. Autoantibodies were assayed by Western immunoblotting using antigens derived from the plasma membrane, cytosol, and nucleus from endometrial and ovarian cells. Natural killer (NK) activity was defined by levels of signaling protein zeta and induction of interferon (IFAT)-gamma following exposure to patients' sera. Patients with endoinctriosis exhibited autoaritibodics reactive with cellular proteins; endometrial membrane proteins exhibited the greatest reactivity, followed by nuclear antigens. In all subcellular fractions, patients ivith stage 3 endometriosis exhibited significantly rnore immunoreactivity than did stage 2 patients, which was greater than that observed in stage 1 patients. The stage-associated increased reactivity resulted from both recognition of additional proteins and enhanced reactivity with shared proteins. Patient sera suppressed NK zeta expression, which resulted in suppression of NK IFN induction. Alterations in autoreactivity and NK activity are observed in endometriosis and may be useful as diagnostic markers, even in early stage disease.