Children with juvenile myelomonocytic leukaemia (JMML) have a poor outcome, with survival in a minority of patients. The major limitation on success of sibling donor bone marrow transplantation for JMML has been reported to be relapse. A total of 46 children with a diagnosis of JMML underwent unrelated donor marrow (URD) transplantation facilitated by the National Marrow Donor Program. Forty-three of 46 patients had neutrophil engraftment at a median of 20 d post transplant, with platelet recovery in 28 of 40 evaluable patients at a median of 34.5 d. Thirty-two of 44 evaluable patients developed acute graft-versus-host-disease (GVHD) (Grades 2-4) and chronic GVHD developed in 14 of 35 evaluable patients. At a median follow-up of 2.0 years, probabilities of survival and disease-free survival were 42% and 24% respectively. The probability of relapse was 58% at 2 years and represents the major cause of treatment failure. Multivariate analysis revealed that chronic GVHD was associated with reduced relapse [risk ratio 0.20 (95% CI 0.04-1.02, P=0.05)] improved survival [risk ratio 0.13 (95% CI 0.03-0.68, P=0.02)] and event-free survival [risk ratio 0.23 (95% CI 0.06-0.94, P=0.04)]. This study demonstrates that relapse is the major cause of treatment failure in patients with JMML undergoing URD transplantation. With lower relapse observed in patients with chronic GVHD, new treatment strategies that focus on enhancing the graft-versus-leukaemia effect may improve survival.