We compared outcome and toxicity in two paediatric groups undergoing SCT and treated with busulphan (BU) by the oral route of administration. One group receiving the standard dose of 1 mg/kg q.i.d. for a total of 16 doses was compared with age- and disease-matched patients receiving 2 mg/kg of BU b.i.d. for a total of eight doses. Seventy-two patients from two Swedish paediatric transplantation centres were included; one centre used a standard q.i.d. administration (n=37) and the second centre used a b.i.d. administration setting (n=35). Our primary objective was to determine the incidence of veno-occlusive disease (VOD), graft-versus-host disease (GVHD), relapse frequency and transplant-related mortality in both cohorts. A total of 17 autologous and 55 allogeneic transplantations was performed for malignant (n=47) and non-malignant (n=25) diseases in the two centres during the period 1990-2005. No significant difference in the incidence of VOD, graft rejection, GVHD, relapse rate or overall survival was observed between the two centres. The clinical outcome of SCT for paediatric patients conditioned with oral BU at a dose of 2 mg/kg for eight doses is comparable to that found for children conditioned using the standard regimen given 1 mg/kg q.i.d. for 16 doses.