Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired disorder of hematopoiesis in which affected cells are deficient in glycosylphosphatidyl-inositol (GPI) anchored surface proteins. The authors used flow cytometry to study 10 patients with PNH. They used a comprehensive panel of monoclonal antibodies against all nine currently known GPI-linked surface proteins (CD14, CD16, CD24, CD48, CD55, CD58, CD59, CD67, CD73) on cells of various lineages. Deficient cells were identified in the granulocytic-monocytic and erythroid lineages in all patients. However, the lymphoid lineage was affected in only eight patients. The patterns of deficiency were variable, with deficient cells constituting a part to all of the cells in the lineages tested. Certain proteins, including CD16, CD58, and CD59, appeared to be preferentially expressed, despite severe deficiencies of other GPI-linked proteins. Moreover, a trimodal pattern of expression of CD16, CD48, and CD59 was observed, in which a population of cells with intermediate levels of expression were identified in addition to positive and deficient cells. The authors' findings indicated a great degree of heterogeneity in the patterns and levels of expression of the GPI-linked proteins in the various cell types, as well as a possible heterogeneity in lineage involvement. The different patterns of expression of GPI-linked proteins should be considered when using flow cytometry to diagnose PNH. Finally, the clinical progression in some of the patients suggested a possible link between PNH, aplastic anemia, and myelodysplasia.