In two neonates, girls, persistent thrombocytopenia was found, which afterwards proved to be caused by a megakaryocytosis. Congenital amegakaryocytic thrombocytopenia is a rare bone marrow failure in young children that is defined as thrombocytopenia with absent or markedly decreased megakaryocytes in the bone marrow. Untreated, amegakaryocytic thrombocytopenia progresses to marrow failure with pancytopenia. Allogeneic stem cell transplantation offers the only possibility for cure, and is successful in approximately half of the patients. Both patients were treated by stem cell transplantation, the one with a matched unrelated donor, the second with stem cells from her HLA-identical sister. The first patient died, the second recovered with a normal number of circulating thrombocytes of donor origin.