Fludarabine-based conditioning (FBC) was given to 24 patients and conventional myeloablative conditioning (MC) to 33 patients, most children, before hematopoietic stem cell transplantation (HSCT) for non-malignant diseases. The donors were human leukocyte antigen (HLA)-A, -B, -DRbeta1-identical related (33%) or unrelated (67%). In the FBC group, two grafts failed versus three in the MC group; all were successfully regrafted. Fever was more common in the MC patients (P=0.003). Bacteremia occurred in 25% of the FBC group and 50% in the MC group (P=0.1). In the FBC group, platelet engraftment was faster and transfusions were fewer (P<0.05). Mucositis and renal function were similar in the two groups. The MC group had higher maximum bilirubin (P=0.03) and less often normal spirometry (P=0.04) after HSCT. A 7-year-old girl in the MC group had permanent alopecia. No patients had severe acute graft-versus-host disease (GVHD). Chronic GVHD was rare. Complete donor CD3+ chimerism was more common in the MC group (P=0.01), but CD33+ engraftment was better with FBS (P=0.03). Treatment-related mortality was 4 and 15%, and 5-year survival was 89 and 85% in the FBC and MC groups. Although survival was similar, FBC is a promising alternative to MC in non-malignant disorders.