The authors describe a boy with Wiskott-Aldrich syndrome (WAS) who was diagnosed immediately after birth using flow cytometric and genetic analysis. At 1 year of age he received unrelated cord blood stem cell transplantation (UCBSCT); however, the sex chromosomes of the peripheral blood mononuclear cells showed that the recipient type was over 70%. This rate gradually increased to over 90% after immunosuppressant therapy was discontinued. Clinical manifestations, including high fever, graft-versus-host disease (GVHD)-like eruptions, and signs of infection recurred. Results of flow cytometric and genetic analysis of mononuclear cells from the boy's mother were normal with no mutation. Three months after UCBSCT, he received an unmanipulated HLA-haploidentical 2-locus-mismatched bone marrow transplant (BMT) from his mother. The prophylaxis against GVHD was tacrolimus and short-term methotrexate. Hematopoietic reconstitution was rapid and fluorescence in situ hybridization analysis revealed sustained engraftment. Grade II acute GVHD developed but improved rapidly with the administration of methylprednisolone. The patient is progressing well and displays complete chimerism 2 years after the BMT. This case suggests that unmanipulated haploidentical BMT from the mother might be feasible not only for malignant disease but also for immunodeficiency disease patients who urgently need stem cell transplants and have no HLA-identical donors.