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Techniques for the diagnosis of invasive fungal infection, including antigen testing, nucleic acid detection and radiological imaging, have improved greatly in recent years. They have the potential to impact on patient management through replacing empirical antifungal strategies with targeted and pre-emptive therapy. Factors that influence performance of these diagnostic tests include underlying disease, the prevalence of fungal infection in particular populations and prophylactic antifungal drug strategies. Understanding these factors is necessary for rational use of antifungal agents and optimal management and prevention of fungal infection in immunosuppressed patients.