Patterns of invasive fungal infections are changing in many ways. Although yeast infections appear to have reached a stable incidence, the number of infections as a result of Aspergillus species appears to be increasing. Especially for mould infection, the diagnosis remains difficult and the detection and identification of clinically relevant isolates to the species level requires new validated techniques. Diagnostic tests are becoming more accurate, with biological markers such as PCR, galactomannan and 1,3 beta-D-glucan undergoing clinical validation. This is of importance because an early diagnosis is associated with increased survival. Correct diagnosis and in vitro susceptibility testing are becoming imperative for guidance of therapy in the context of changing epidemiology and the emergence of acquired resistance to antifungal drugs, as is insight into host factors that increase susceptibility to invasive mould infection and into the risks associated with new treatment modalities of underlying diseases. Despite improvements in the survival rates of patients with invasive fungal infection in recent years, continued research is required to meet the challenges associated with changes in epidemiology and resistance development.