For patients with well-characterized, rapidly fatal, nonmalignant immunodeficiency disorders, such as SCID, the decision to proceed with allogeneic SCT is clear-cut. For patients with many other disorders, this decision can be extremely difficult. Disorders such as LAD or CGD have a variable natural history. Each patient must be considered individually, with the risk for SCT-related morbidity and mortality carefully weighed against that of the underlying disease. Significant advances during the past 10 years have made SCT a much safer procedure. Use of nonmyeloablative conditioning regimens as a means of reducing toxicity of high-dose chemotherapy and irradiation hold great promise. Highly immunosuppressive, nonchemotherapeutic agents that inhibit graft rejection or GVHD by blocking the critical costimulatory component of the T-cell receptor-antigen interaction are beginning to emerge and may be ideal for SCT of nonmalignant diseases. Therefore, the risk-benefit equation must be reassessed each year as the severity of patients' disorders is better defined and techniques of SCT improve.