This single-centre, retrospective, observational pilot study was performed to evaluate the safety and efficacy of intravenous and oral itraconazole prophylaxis in paediatric haematopoietic stem cell transplantation (HCT). Study end-points were proven invasive fungal infection (IFI), survival, adverse reactions and graft-vs.-host disease (GVHD); 53 children and one young adult (median age 8.6 yr; range 0.4-18.3) transplanted between November 2001 and August 2004 were included in this study. Itraconazole was given intravenously from day +3 after HCT until oral medication became possible and continued until day +100 after HCT. Two proven new IFI in the itraconazole group (candidiasis, n = 1; aspergillosis, n = 1) were observed. After a median follow-up of 1.6 yr (0.3-6.1), six deaths (8%) were seen; 24 patients (45%) developed GVHD degree I-II, three children (6%) had GVHD degree III-IV. In 11 of 53 patients (21%), itraconazole prophylaxis was discontinued prematurely, mostly because of fever of unknown origin (n = 7). In total, 21 of 53 (40%) of the children had abnormal results of laboratory investigations during the prophylaxis. The results of this pilot study indicate that itraconazole prophylaxis during HCT in children is feasible and safe, despite abnormal laboratory results. The efficacy in terms of prevention of IFI, however, has to be addressed in a prospective large-scale study.