The aim of this study was to determine changes in the incidence of nosocomial candidaemia and to evaluate the risk factors, demographic features, treatment and clinical outcome associated with candidaemia in a Turkish tertiary care paediatric unit within a 9-year period. The data of children who were diagnosed as nosocomial candidaemia, were examined in this study. Between January 1997 and December 2005, a total of 102 nosocomial candidaemia episodes were identified in 102 patients. The rate of nosocomial candidaemia in our clinic increased from 3.2 cases per 1000 admissions in 1997-1999, to 5.5 per 1000 admissions in 2000-2002 and to 6.9 per 1000 admissions in 2003-2005 (P = 0.003). The species most frequently causing candidaemia were Candida albicans (39.2%), Candida parapsilosis (21.6%) and Candida tropicalis (15.7%). The mortality of C. albicans (37.5%), was significantly higher than the mortality of non-albicans species (17.7%) (P = 0.04). Independent risk factors associated with candidaemia-related deaths by logistic regression analysis were disseminated candidiasis (odds ratio, 5.7; P = 0.01), paediatric intensive care unit stay (odds ratio, 8.1; P = 0.001), prolonged antibiotics therapy (odds ratio, 5.2; P = 0.014), use of total parenteral nutrition (odds ratio, 4.4; P = 0.038) and mechanical ventilation (odds ratio, 4.9; P = 0.01). The rate of nosocomial candidaemia in our clinic increased > 2-fold during the study period.