Myelodysplasia (MDS) and aplastic anaemia-paroxysmal nocturnal haemoglobinuria (AA/PNH) syndrome developed in a severe aplastic anaemia (AA) patient after treatment with immunosuppressive (IS) therapy. Glycosylphosphatidyl inositol (GPI)-linked proteins were determined, and during the AA/PNH phase, a high proportion of neutrophils were found to be negative, without clinical evidence of haemolysis. However, MDS developed with cytogenetic abnormalities of monosomy 7,9q- and a rearranged chromosome 6; the GPI-linked protein negative cells were completely replaced by positively expressing cells. This represents the emergence of a GPI-linked protein positive myelodysplasia clone arising separately from an AA/PNH clone.