Paroxysmal nocturnal hemoglobinuria (PNH) is an uncommon acquired stem cell disorder associated with periodic hemolytic events. This benign clonal disease is caused by abnormalities of the X-linked phosphatidylinositol glycan class A (PIGA) gene and is associated with cytopenias and thrombosis. Although the trilineage of bone marrow elements is affected, involvement of the red blood cell (RBC) line was recognized first due to its abnormal sensitivity to complement-mediated intravascular hemolysis. Totally or partially deficient blood cell membrane proteins include decay accelerating factor (DAF, CD55), membrane inhibitor of reactive lysis (MIRL, CD59), and other proteins attached to the glycophosphatidylinositol (GPI) spine. Stem cell transplantation can be curative in PNH. Diverse laboratory abnormalities observed in PNH include bone marrow hyper- and hypoplasia, hematologic cytopenias, micro- and macrocytosis, decreased leukocyte alkaline phosphatase (LAP), hemoglobin- and hemosiderinuria, as well as associated iron deficiency. The more definitive laboratory tests comprise older biochemical and newer flow cytometric (FCM) procedures. The former group includes the sucrose hemolysis test for screening and Ham's acid hemolysis test for confirmation; the latter group includes FCM analyses of CD55 and CD59, which have recently replaced Ham's test, and FCM quantification of specific GPI-anchor binding using fluorescent-labeled inactive toxin aerolysin (FLAER). FLAER is more sensitive than FCM quantification of antibody-binding to CD59 for PNH diagnosis.