A 12-year-old girl with Fanconi anaemia (FA) received a bone marrow transplant from her HLA-identical brother following conditioning with cyclophosphamide (20 mg/kg), thoraco-abdominal radiation (TAI) (4 Gy) and equine anti-thymocyte globulin (ATG) (90 mg/kg). Engraftment was delayed and initially tenuous, and was followed by mixed chimerism (MC) over a follow-up period of 2 years. DNA analysis of engraftment was performed on whole peripheral blood and on separated granulocytes, B and T lymphocytes using PCR detection of CA tandem repeat polymorphisms. At 10 weeks post BMT, granulocytes were predominantly donor, but B and T lymphocytes recipient, in origin. Over the subsequent 90 weeks, granulocytes and B lymphocytes were donor-derived, whilst T cells showed persistent MC but with an increasing donor component. Marrow haemopoietic function (Hb, ANC and platelet count) improved gradually in parallel with a rise in the proportion of donor lymphocyte engraftment. We postulate that a population of recipient lymphocytes survived conditioning and in turn delayed the development of full donor chimerism. Although transient MC has been described after allogeneic BMT in FA, its association with delayed engraftment, and persistence for more than 1 year post BMT, has not been documented clearly.