Paroxysmal nocturnal hemoglobinuria (PNH) is a unique clonal stem cell disorder characterized by intravascular hemolysis, thrombotic events and bone marrow failure. There has been accelerated progress in understanding the mechanisms underlying the clinical features of the disease over the last decade. The development of PNH requires not only a somatic mutation of the phospatidylinositol glycan complementation class A (PIG-A) gene, but also a survival advantage of the PNH clone ('dual pathogenesis' theory). There is increasing evidence that negative selection against the non-mutated cells rather than positive selection of the PIG-A gene mutant cells is responsible for the dominance of the PNH clone. In this review, we summarize the important advances in the understanding of PNH, but we also concentrate on the presence of PNH clones in other hematological disorders, including aplastic anemia (AA), myelodysplastic syndromes (MDS), acute leukemias, and myeloproliferative and lymphoproliferative syndromes. The fuller comprehension of the pathophysiology of PNH may have wider implications than for PNH itself, as indicated by the presence of PNH clones in these hematological malignancies, and by the therapeutic implications of this fact, as already described in patients with AA and MDS.