Paroxysmal nocturnal hemoglobinuria (PNH) is considered to be a clonal disorder, although most investigations have failed to show chromosomal abnormalities. The present patient suffered from PNH and exhibited in bone marrow cells two abnormal clones with 47 chromosomes in addition to cells with 46 chromosomes. One clone showed trisomy 9, a finding previously reported in leukemias and myeloproliferative disorders. Thus, PNH seems to be a clonal myeloproliferative disease.