Non-malignant hematologic disorders (NMHD) of childhood comprise a variety of disorders including acquired severe aplastic anemia, and inherited marrow failure syndromes. Patients with high risk NMHD without matched related donors fare poorly with allogeneic hematopoietic alternative donor stem cell transplantation (allo-HSCT) and are at high risk for developing graft versus host disease following unmodified grafts. We retrospectively analyzed data on 18 patients affected by NMHD, lacking an HLA-identical sibling donor, who underwent an alternative donor allo-HSCT at our institution between April 2005 and May 2013. 50% had received prior immunosuppressive therapy, 72% had a history of infections, and 56% were transfusion-dependent at the time of transplant. Cytoreduction included a combination of three of five agents: fludarabine, melphalan, thiotepa, busulfan and cyclophosphamide. Grafts were T-cell depleted. All evaluable patients engrafted. Five died of transplant complications. The cumulative incidence of graft versus host disease was 6%. No patient had recurrence of disease. 5-year overall survival was 77%. Age at transplant <6 years was strongly associated with better survival. Based on these results, transplant with chemotherapy-only cytoreductive regimens and T-cell depleted stem cell transplants could be recommended for patients with high risk NMHD especially at a younger age.