The clinical outcome of 3 myelodysplastic syndrome (MDS) patients with polyclonal hematopoiesis is reported. All patients were heterozygous for the phosphoglycerate kinase (PGK) gene. The presence of polyclonal hematopoiesis was determined by the X-chromosome-linked restriction fragment length polymorphism-methylation method using the PGK gene as a marker. The patients were initially diagnosed as having refractory anemia (RA), RA with ring sideroblasts (RARS), and RA with an excess of blasts (RAEB), respectively. Their pancytopenia persisted during the follow-up period of 11.4 years for the RA patient, 19.5 years for the RARS patient and 0.8 years for the RAEB patient. Although the RARS patient continues to be in good health, leukemic transformation occurred in the other 2 patients. A karyotype change from 46,XX to 45,XX,t(3;21),-7 was observed at the time of disease progression in the RA patient. The coexistence of a monoclonal MDS clone and normal bone marrow cells is thought to be the most probable reason for the polyclonal hematopoiesis of these patients.