Paroxysmal Nocturnal Hemoglobinuria (PNH) is an acquired hemolytic anemia characterized by chronic hemolysis, deep thrombosis, and hypoplastic marrow, and thought to be a clonal hematopoietic stem cell disorder. Affected blood cells are deficient in glycosylphosphatidylinositol (GPI)-anchored cell surface proteins. Recent investigations revealed that the PIG-A gene, which participates the biosynthesis of the GPI-anchor, was identified and the mutations were detected in the patients with PNH. Here we discuss the following problems related to the PIG-A gene; (1) the inconsistency of the expression of the GPI-anchored proteins and the mutations of the PIG-A gene, (2) the existence of the multiple PNH clones bearing different PIG-A mutations in a single patient, (3) aplastic anemia-PNH syndrome and PIG-A gene.