Objective Estrogens influence many physiologic processes and are also implicated in the development or progression of numerous diseases, including autoimmune disorders. Aberrations of lymphocyte homeostasis that lead to the production of multiple pathogenic autoantibodies, including autoantibodies specific to estrogen receptor (ER), have been detected in the peripheral blood of patients with systemic lupus erythematosus (SLE). This study was undertaken to assess the presence of both anti-ERa and anti-ER beta antibodies in sera from patients with SLE, to analyze the effect of these antibodies on peripheral blood T lymphocyte homeostasis, and to evaluate their role as determinants of disease pathogenesis and progression. Methods. Anti-ER antibody serum immunoreactivity was analyzed by enzyme-linked immunosorbent assay in samples from 86 patients with SLE and 95 healthy donors. Phenotypic and functional analyses were performed by flow cytometry and Western blotting. Results. Anti-ER alpha antibodies were present in 45% of the patients with SLE, whereas anti-ER alpha antibodies were undetectable. In healthy donors, anti-ER alpha antibodies induced cell activation and consequent apoptotic cell death in resting lymphocytes as well as proliferation of anti-CD3-stimulated T lymphocytes. A significant association between anti-ER alpha antibody values and clinical parameters, i.e., the SLE Disease Activity Index and arthritis, was found. Conclusion. Our data suggest that anti-ER alpha autoantibodies interfere with T lymphocyte homeostasis and are significantly associated with lupus disease activity.