Paroxysmal nocturnal hemoglobinuria (PNH) is a rare acquired hematopoietic stem cell disorder closely related to aplastic anemia. Hemolytic anemia and life-threatening thromboses are common features in many patients. Rapid diagnosis is highly desirable and flow cytometry plays a key role in the laboratory investigation of PNH. By demonstrating absence of cell membrane glycosylphosphatidylinositol-anchored proteins from granulocytes or red cells, a definitive diagnosis of PNH can be established. This can have a considerable impact on patient management and outcome. As with all rare diseases, internal and external quality assurance is essential for good laboratory practice and to fulfill the requirements of national laboratory accreditation schemes.