Data on the epidemiology of invasive Candida infections in paediatric patients in Europe are still limited. The aim of this retrospective study was to analyse the epidemiology of candidaemia in a tertiary paediatric hospital in Poland from 2000 to 2010. Using microbiological records, a total of 118 episodes of candidaemia were identified in 114 children, with an annual incidence of 0.35 episodes/1000 discharges. The highest incidences were found in the medical intensive care unit (5.28), and in neonatal intensive care (1.47). The mortality rate was 8.5%. Candida albicans and C. parapsilosis were the most prevalent species (39.8% and 35.6% respectively). The prevalence of non-albicans species increased from 12.5% in 2000 to 70% in 2010. No differences were found between C. albicans and C. non-albicans episodes in terms of demographics, risk factors or mortality. The highest resistance rates (overall 7.6%) were observed for fluconazole (4.3% in C. albicans, 7.1% in C. parapsilosis and 13.8% in other Candida species). Resistance to amphotericin B (2.5%) was limited to non-albicans isolates. The dynamic changes in species distribution and increasing resistance of fungal pathogens confirm the importance of epidemiological surveillance.