Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hemolytic anemia in which abnormal red blood cells with enhanced susceptibility to complement undergo intravascular hemolysis when complement is activated in vivo, resulting in hemoglobinuria. This enhancement of complement susceptibility appears to involve multipotent stem cells and, in this respect, is thought to closely resemble myelodysplastic syndrome. Recently, it has been reported that the increased susceptibility of PNH cells to complement-mediated lysis is related to a deficiency of complement regulatory membrane proteins, especially CD55 and CD59. Both proteins are glycosylphosphatidylinositol (GPI)-anchored membrane proteins. It was found that a deficiency of GPI-anchored membrane proteins in PNH cells is due to the faulty synthesis of the GPI-anchor which may occur during early synthesis. Moreover, it is suggested that an abnormality of the PIG-A (phosphatidylinositol glycan-class A) gene, which is related to the early stage of GPI-anchor synthesis, is responsible for the pathogenesis of PNH. In conclusion, the clinical expression of PNH is dependent on two factors, complement susceptibility of PNH blood cells and changes in bone marrow function. The search for the ideal treatment of this disease may be aided by resolving the relationship between the two.