Hematopoietic stem cell transplantation (HSCT) is the treatment of choice for Wiskott-Aldrich syndrome (WAS). The aim of this retrospective study is to report the effect of the conditioning regimen and donor source on disease-free survival (DFS) in children undergoing HSCT for WAS. Fourteen children who underwent HSCT at 4 Israeli centers from 1996 to 2011 were included in this study. Five children were transplanted from matched related donors (4/5 siblings, 1/5 fully matched uncle) and other donors were used in 9 children. Six patients were conditioned with full dose busulfan/cyclophosphamide (Bu/Cy) whereas 8 patients were conditioned with other regimens. Thirteen of 14 patients (92.8%) are alive with a median follow-up of 3.4 years (range, 5 mo to 12.5 y). Nine patients (64.3%) survive with complete clinical, immunologic, and hematologic recovery. Children conditioned with full dose Bu/Cy had a 100% DFS, compared with children conditioned with other regimens, 25%±19% (P=0.022). Donor source was not associated with DFS. Graft failure was related to the use of conditioning regimens other than full dose Bu/Cy and not to the donor source. Further studies are required to determine the best conditioning regimen and optimal donor source for children with WAS.