To determine if high-dose cyclophosphamide is an effective therapy for children with refractory severe aplastic anemia (SAA). SAA is an illness characterized by the depletion of hematopoietic precursors associated with life-threatening complications. Hematopoietic stem cell transplant (HSCT) is the treatment of choice if a human leukocyte antigen (HLA)-related donor is available. Immunosuppression with anti-thymocyte globulin (ATG) and cyclosporine A (CSA) is an option for patients who are not HSCT candidates. Unrelated donor HSCT has been used with limited success. High-dose cyclophosphamide has been used successfully in the treatment of adults with SAA, but experience in children is limited. Five pediatric patients who had failed previous immunosuppressive therapy for SAA were treated with high-dose cyclophosphamide (45 mg/kg/day x 4 days). After 12 months of treatment, two of five patients experienced a complete response with high-dose cyclophosphamide therapy. The two complete responders achieved red cell recovery with a hematocrit of >36% at days 212 and 112 and platelet recovery with a platelet count of >100 x 10(9)/L at days 126 and 324. Of the remaining patients, one patient failed to respond, and two patients expired from infectious complications. High-dose cyclophosphamide can lead to complete responses in children with SAA who have failed to respond to traditional immunosuppressive therapy.