Bone marrow failure (BMF) syndromes include a broad group of diseases of varying etiologies, in which hematopoeisis is abnormal or completely arrested in one or more cell lines. BMF can be an acquired aplastic anemia (AA) or can be congenital, as part of such syndromes as Fanconi anemia (FA), Diamond Blackfan anemia, and Schwachman Diamond syndrome (SDS). In this review, we first address the evolution and current status of bone marrow transplantation (BMT) in the pediatric population in the most common form of BMF, acquired AA. We then discuss pediatric BMT in some of the more common inherited BMF syndromes, with emphasis on FA, in which experience is greatest. It is important to consider the possibility of a congenital etiology in every child (and adult) with marrow failure, because identification of an associated syndrome provides insight into the likely natural history of the disease, as well as prognosis, treatment options for the patient and family, and long-term sequelae both of the disease itself and its treatment.