Although invasive fungal infections (IFIs) are relatively rare, they are important causes of morbidity and mortality in immunocompromised pediatric patients. Early and precise diagnosis of IFI is important to allow antifungal treatment to be started in time and to reduce the unnecessary use of toxic antifungal agents. Although traditional approaches such as direct microscopic examination, histopathological evaluation and cultivation are still gold standard, the diagnosis of IFI is generally difficult because of inadequate sensitivity and specificity with these tests. Commercial systems detecting the Aspergillus cell wall antigen galactomannan and 1,3-β-D-glucan are seen as the most convenient nonculture methods for the diagnosis of the IFI and monitoring of antifungal treatment. Several molecular methods have been described for the diagnosis of opportunistic mycoses. However, they have not been standardized and have only been used in experimental studies.