During the last 20 years rising prevalence of invasive fungal infections, mainly candidiasis or aspergillosis, are observed in paediatric intensive care units. Infections caused by Candida non-albicans species are a particular problem. Results of treatment depend on fast and correct diagnostics, avoidance of risk factors and selected pharmacotherapy. The local epidemiological situation as well as patient factors should be taken into consideration during treatment. Current recommendations for the diagnosis and strategy of choosing treatment options for invasive fungal infections in paediatric intensive care units are presented.