Paroxysmal nocturnal hemoglobinuria (PNH) is characterized by absence of CD55 and CD59 from the surface of affected cells. PNH has been associated with myelodysplastic syndromes (MDS). The aim of our study was to estimate the prevalence of the PNH clone in MDS patients by detecting CD55 and CD59 deficiency. We studied 90 MDS patients: 19 patients with RA, 15 with refractory anemia with ringed sideroblasts (RARS), 18 with refractory anemia with excess of blasts (RAEB), 17 with refractory anemia with excess of blasts in transformation (RAEB-t), and 21 with chronic myelomonocytic leukemia (CMML). Twenty healthy individuals were also studied as the control group. We studied the PNH clone on granulocytes of these patients with the aid of flow cytometry. CD55- and CD59-deficient granulocytic populations were detected in 15.5% of MDS patients compared to 2.8% of normal individuals. Among the subgroups of the study, significant difference was present in three cases: (1) between CMML and control, (2) between CMML and RA, and (3) between CMML and RARS. These data indicate a possible association between PNH phenotype and MDS. MDS patients of worse prognosis (CMML) express more strongly the PNH clone compared to those of better prognosis (RA and RARS). Perhaps, the examination of MDS patients for the PNH clone by flow cytometry could provide us with a valuable prognostic tool.