Patients with hemophagocytic lymphohistiocytosis, Chediak Higashi syndrome, X-linked lymphoproliferative syndrome, severe progressive Langerhans cell histiocytosis, or other primary immunodeficiencies with complications of hemophagocytosis receive busulfan IV over 2 hours every 6 hours on days -9 to -6, cyclophosphamide IV over 2 hours on days -5 to -2, etoposide IV over 22 hours on days -5 to -3, and ATG IV twice daily on days -2, -1, 1, and 2. Allogeneic bone marrow or umbilical cord blood transplantation takes place on day 0. Patients receive graft versus host disease (GVHD) prophylaxis with methotrexate IV on days 1, 3, 6, and 11 and cyclosporine IV on days -3 to 50.