Langerhans cell histiocytosis (LCH) that is refractory to conventional chemotherapy has a poor outcome. Hematopoietic stem cell transplantation (SCT) is a promising approach for refractory LCH because of its immunomodulatory effect. In this study, the outcomes of children with refractory LCH undergoing SCT in Japan were analyzed. Between November 1995 and March 2007, 15 children younger than 15 years (9 males, 6 females) with refractory LCH underwent SCT. The patients' median age at diagnosis was 8 months (range, 28 days to 28 months), and all had failed conventional chemotherapy. The median age at SCT was 23 months (range, 13-178 months). Nine had risk organ involvement at diagnosis, including liver (n=6), spleen (n=5), lung (n=5), and/or hematopoietic system (n=4). For SCT, a myeloablative regimen was used for 10 patients, and a reduced-intensity conditioning regimen (RIC) was used for five. The donor source varied among the patients, but allogeneic cord blood was primarily used (n=10). Subsequently, 11 of 15 patients have survived with no evidence of disease, with a 10-year overall survival (OS) rate (median+/-standard error) of 73.3+/-11.4%. The 10-year OS rate of nine patients with risk organ involvement at diagnosis was 55.6+/-16.6%, whereas six without risk organ involvement have all survived with no evidence of disease (P=0.07). These results indicate that SCT is promising as a salvage approach for children with refractory LCH.