A 3-year-old girl with severe aplastic anemia (SAA) that was unresponsive to steroid, cyclosporine and filgrastim treatments received bone marrow (BM) mesenchymal stromal cells (MSC; 1.25 x 10(6)/kg), granulocyte colony-stimulating factor (G-CSF)-mobilized BM and peripheral blood stem cell grafts from her father. Prior to stem cell transplantation, she had experienced repeated bacterial infections and received 44 blood transfusions during 8 months after diagnosis. The conditioning regimen consisted of fludarabine, cyclophosphamide and busulfan, and prophylaxis of acute graft-versus-host disease (GvHD) was performed by administration of anti-CD25 monoclonal antibody, cyclosporine A, methotrexate, mycophenolate mofetil and anti-thymocyte globulin. The patient achieved rapid hematopoietic engraftment of donor origin and no acute or chronic GvHD was observed. She is now alive with a good performance status, and the dose of cyclosporine A is being tapered. The novel regimen described here might be a suitable option for children with SAA who lack immediate access to HLA-matched sources.