Children with acute lymphoblastic leukaemia (ALL) receiving haematopoietic stem cell transplantation (HSCT) in third complete remission (CR3) are at high risk for transplant-related mortality (TRM) and relapse. Twenty-two consecutive children with ALL in CR3 received HSCT between January 1994 and August 2005. Ten patients died of TRM, seven patients relapsed, six did not have graft-versus-host disease (GVHD). Five patients were long-term survivors, (median follow-up, 5.8 years; range 2.9-11.7). Three-year event-free survival was 0.32 (95% confidence interval 0.19 and 0.59). Survivors had moderate to severe GVHD. Allowing some GVHD or exploring means of inducing GVHD should be considered in CR3 patients.