A case of myelodysplastic syndrome (MDS) complicated by septic pulmonary embolism is reported. A 61-year-old female who had been followed for refractory anemia with excess of blasts suddenly died of acute respiratory failure. An autopsy revealed massive pulmonary emboli with gram-positive cocci gathered in the emboli and alveolar spaces. Staphylococcus aureus was also detected through a blood culture from the right atrium. We speculate that pulmonary embolism was the result of septicemia induced by the immunosuppressive condition associated with MDS.