A 13-year-old girl presented with two spontaneously reversible episodes of marrow hypoplasia. She subsequently developed acute lymphoblastic leukaemia (ALL) 8 months later. Southern analysis showed identical clonal immunoglobulin heavy chain gene rearrangement bands in the leukaemic cells as well as the marrow cells obtained at the two hypoplastic episodes. Hypoxanthine phosphoribosyl transferase polymorphism studies showed that the ALL blast cells, bone marrow and peripheral blood cells during the two hypoplastic episodes all exhibited clonal haematopoiesis with the same X-chromosome inactivated. This case provides strong evidence that aplastic anaemia and ALL may represent evolution of the same abnormal clone.