Fanconi anaemia (FA) is a rare genetic disease characterized by chromosomal instability, somatic abnormalities, marrow failure and cancer proness. The main cause of morbidity and mortality is bone marrow failure, which typically arises in the first decade of life and progresses to full-blown transfusion dependence and severe neutropenia in a variable number of years. Myelodysplastic syndrome (MDS) and AML may arise on the background of marrow failure, although cases of patients diagnosed with MDS or overt leukaemia before the full appearance of marrow aplasia are reported. This article reviews the current options for treatment of bone marrow failure in FA and provides an algorithm for supporting decisions on treatment. The use of androgens, corticosteroids and growth factors is reviewed, as well as the results in recent cohorts of matched sibling donor haematopoietic stem cell (HSC) transplants and unrelated donor HSC transplants, including cord blood graft. The conditioning regimens used are analysed and commented. Up-to-date information on second tumours after HSC transplant and on experimental treatments such as gene therapy, prenatal and preimplantation diagnosis and inhibition of pro-inflammatory cytokines is provided.