Sixty-four pediatric patients who underwent allogeneic (n = 35), autologous (n = 28) or syngeneic (n = 1) bone marrow transplantation (BMT) between 1992 and 1994 were evaluated retrospectively. As antifungal prophylaxis, all patients received amphotericin B tablets and 62 of 64 (96.9%) received oral fluconazole. Weekly surveillance cultures revealed fungal colonization in 35 patients (54.7%). Six patients (9.4%) were colonized before BMT only, 17 (26.6%) after BMT only and 12 (18.8%) both before and after BMT. Candida albicans was the most frequently isolated fungus [21 of 46 fungal isolates (45.7%)], followed by C. glabrata [14 isolates (30.4%)]. Non-albicans species of Candida were most frequently isolated after BMT from the faeces, often in high numbers. Autologous marrow recipients had a higher fungal colonization rate both before and after BMT than allogeneic marrow recipients. One patient suffered from invasive pulmonary aspergillosis after BMT. No fungaemis or deep-seated yeast infections were observed. Six of the seven patients who had to be treated with intravenous amphotericin B because of antibiotic-refractory fever had undergone autologous BMT. Multivariate analysis of various parameters showed only pre-BMT yeast colonization to be independently associated with post-BMT colonization. Thus, systemic mycoses occurred only rarely in this study population; however yeast colonization after BMT (especially with non-albicans species) was a frequent in spite of double prophylaxis with oral amphotericin B and fluconazole.