A patient with paroxysmal nocturnal hemoglobinuria (PNH) received a syngeneic peripheral blood stem cell transplant (PBSCT) with high-dose cyclophosphamide (CY) conditioning. He had a reasonable engraftment and complete hematologic recovery. However, at 12 months after PBSCT, he became symptomatic and peripheral blood cells were almost entirely composed of glycosylphosphatidylinositol-anchored proteins deficient cells. This case suggests that high-dose CY may not exert a significant effect on PNH clones in the long term, although it had been effective in allogeneic BMT. In view of the possible autoimmune basis, it seems to be necessary to include other immunosuppressive therapy including ALG in addition to CY.