A total of 201 cases of fungaemia in children in a 12-year national survey from seven University Paediatric Clinics in Slovakia in 1990-2001 was assessed to determine risk factors, therapy and outcome, and to compare those cases with fungaemia in 130 adult cancer patients studied in a similar survey. Four univariate analyses were performed to assess differences in aetiology, antifungal susceptibility and outcome between fungaemia in neonates and paediatric intensive care unit (ICU) patients as well as between paediatric and adult cancer patients with fungaemia. There was a significant difference in aetiology and antifungal susceptibility between the subgroups of children with fungaemia: 83.3% of neonates versus 40.2% in children with cancer were due to Candida albicans. None of the non-albicans Candida spp. (NAC) in neonates but 23.5% of NAC isolates from children with cancer were resistant to fluconazole. C. albicans caused 144 (71.1%) episodes and NAC 48 (23.7%) episodes. Trichosporon beigelii, Blastoschizomyces (Trichosporon) capitatus, Rhodotorula rubra and Cryptococcus laurentii were found less frequently in neonates than in children with cancer (18.8%). There were not many differences in risk factors between paediatric fungaemia and adult cancer fungaemia except C. albicans aetiology, corticosteroid use in therapy, breakthrough fungaemia after ketoconazole prophylaxis and meningitis as a complication, which were observed significantly more frequently among children than in adults, both with cancer and fungaemia. Thirty-three of the paediatric fungaemias were breakthrough cases and appeared frequently in children with cancer. Fifty-one (25.1%) children died with fungaemia (attributable mortality) and 25 (12.7%) due to underlying disease with fungaemia; overall mortality was 37.8% and there was no significant difference in death rates between the subgroups of paediatric patients (neonates, children in ICUs and children with cancer).