Some patients with paroxysmal nocturnal haemoglobinuria (PNH) have bone marrow findings characteristic of myelodysplastic syndrome. We studied nine PNH patients to determine whether these karyotypic abnormalities were more likely to occur in glycosylphosphatidylinositol‐anchored protein (GPI‐AP)‐negative cells. Abnormal chromosome patterns were evident only in the GPI‐AP‐positive populations of the PNH clone in 8 of 9 cases studied. Purified GPI‐AP‐negative CD34 cells gave rise only to cells of normal karyotype, whereas the progeny of the GPI‐AP‐positive CD34 cells showed the karyotypic abnormality. These findings suggest that environmental factors, but not genetic instability of the GPI‐AP‐deficient clone, foster development or survival of haematopoietic cells with chromosomal abnormalities.