We successfully treated a 33-year-old woman with etoposide who developed systemic sclerosis (SSc)-associated refractory hemophagocytic syndrome (HPS). She had been diagnosed as SSc because she had had Raynaud's phenomenon, proximal scleroderma, telangiectasia, microstomia, thickening and shortening of lingual frenulum and positive antinuclear antibody since 1994. In September 1999, she showed high fever, anemia, thrombocytopenia, elevation of serum lactate dehydrogenase (LDH) and ferritin levels and hemophagocytosis in her bone marrow, which led to the diagnosis of HPS. Her symptoms were improved by 40 mg of daily oral prednisolone (PSL). While tapering PSL, she complained right coxalgia and magnetic resonance image (MRI) depicted avascular necrosis (AVN) of right femoral head. In May 2000, she again suffered from HPS when she was taking 19 mg of PSL daily. To avoid the development of another AVN of her bone, she was treated with monthly cyclophosphamide (CPA) pulse therapy (300-400 mg/day). Although her HPS transiently ameliorated with CPA, it flared up again with high fever, general fatigue, severe pancytopenia and extremely high serum LDH and ferritin levels after the 4th CPA pulse therapy. She was admitted again to our hospital and PSL was increased to 40 mg daily which did not improve HPS. We, therefore, treated her with intravenous etoposide (100 mg/day, three consecutive days) along with granulocyte-colony stimulating factor (G-CSF). She developed transient bone marrow suppression, but her laboratory data gradually normalized within two weeks and she became afebrile after 18 days of etoposide administration. This is the first case in the literature which suggests the efficacy of etoposide against refractory autoimmune-associated hemophagocytic syndrome.