OBJECTIVE Invasive fungal infections are an escalating problem in paediatrics. The purpose of this review is to update the recent evidence on antifungal treatment options as well as to provide an outline of best practices in treating children. RESULTS Candida and Aspergillus species are the leading causes of invasive fungal infections in paediatric patients. Invasive fungal infections are associated with significant morbidity and mortality and preemptive antifungal therapy has been found to improve survival. Although novel antifungal agents (echinocandins and second generation triazoles) and treatment strategies based on surrogate markers (galactomannan and beta-glucan) have established utility in treating adults, limited data are available to guide paediatricians when managing children with invasive fungal infections. The collective findings of the up-to-date data show that treatment recommendations are similar for paediatric and adult patients. Progress has been made in describing pharmacokinetics and safety of voriconazole and echinocandins, respectively, while further efficacy, safety and pharmacokinetic trials are ongoing. CONCLUSIONS The current guidelines, proposed mainly for adults with invasive fungal infections, are likely applicable also to paediatric patients, but prior to making definitive recommendations more pharmacokinetic and phase III trials are needed.