A 25-year-old man was admitted for evaluation of pancytopenia on May 2, 1997. On admission, he had pancytopenia with a normal reticulocyte count. Bone marrow aspirate specimens displayed a normal karyotype and hypocellularity without myelodysplasia. Although total bilirubin and lactate dehydrogenase levels were within their normal ranges, the haptoglobin level was low; additionally, two-color flow cytometric analysis determined that 3.3% of erythrocytes were double-negative for CD55 and CD59 expression. Atypical paroxysmal nocturnal hemoglobinuria with bone marrow hypoplasia was diagnosed. Because initial treatment with cyclosporin A was not effective, the patient was subsequently given a combination of antithymocyte globulin, cyclosporin A, and granulocyte colony-stimulating factor. Although the pancytopenia subsided, the percentage of double-negative erythrocytes in the patient's blood remained almost unchanged compared to findings obtained on admission.