Congenital amegakaryocytic thrombocytopenia is an extremely rare disorder for which bone marrow transplantation offers the only possibility for cure. The pathophysiology is unclear. Two children with familial amegakaryocytic thrombocytopenia underwent unrelated donor transplantation (bone marrow in one, umbilical cord blood in the second) after a preparative regimen of cyclophosphamide and total body irradiation. Both patients failed initial engraftment, required further donor stem cell infusions and are currently well with sustained engraftment, 16 months and 7 months after transplantation, respectively. The difficulty in achieving engraftment of unrelated donor stem cells in these children suggests that in future cases additional measures to achieve engraftment may be necessary, for example, a more aggressive preparative regimen or an increased stem cell dose.