We analyzed the clinical course and outcome in 50 patients (27 males, 23 females) suffering from aplastic anemia (AA), treated in our department between 1987 and 2007. The median age was 37 years (range: 14–70 years). A total of 42 patients received antithymocyte globulin and cyclosporine A (CSA). Seven patients were transplanted using a matched sibling donor upfront, and one patient was treated with CSA and growth factors only. A total of 34 patients (68 %) achieved a complete remission, and 7 (14 %), a partial remission. Eight patients (16 %) did not respond to treatment, and one died shortly after transplantation. Relapses of AA occurred in eight patients (20 %). No obvious correlations between clinical parameters, including age, karyotype, existence of paroxysmal nocturnal hemoglobinuria clones, pretreatment blood counts, progenitor cell counts, and the response to immunosuppressive therapy (IST), were found. We also examined the numbers of colony-forming progenitor cells (CFUs) before and after therapy. In most responding patients, CFU numbers increased substantially after successful therapy. However, even in patients without a substantial increase in CFU, stable remissions were observed. Together, both IST and stem cell transplantation are reasonable treatment options for patients with AA.