Therapy-related myelodysplastic syndrome (t-MDS) is a very rare complication of allogeneic bone marrow transplantation (BMT). A woman with T acute lymphoblastic leukaemia (T-ALL) received an allogeneic BMT from a donor with the beta-thalassaemic trait. Five years after BMT, the red cell indices returned to normal after an initial conversion to microcytosis, implying autologous haematopoietic regeneration. Seven years after BMT, thrombocytopenia developed and marrow examination confirmed t-MDS, with a characteristic karyotype 46,XX,inv(3)(q21;q26), del(5)(q13),add(17)(p11). Retrospective molecular analysis of donor/recipient chimaerism showed gradual regeneration of recipient cells after BMT, culminating at the time of t-MDS. Our findings illustrate the unusual occurrence of t-MDS after allogeneic BMT. Re-emergence of recipient haematopoesis may herald the development of a haematological malignancy different from the original neoplastic clone for which the BMT was performed.