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Despite advances in the diagnosis and management, invasive fungal diseases contribute substantially to the morbidity and mortality of patients with prolonged neutropenia.Major advances in the prevention, diagnosis, and treatment of invasive fungal diseases have occurred with the introduction of fungal markers and new antifungal agents over the past decade. The newer broad-spectrum azoles and echinocandins, due to their acceptable safety profiles and efficacy, have emerged as valuable options as antifungal prophylaxis and therapy. Empirical antifungal therapy, a strategy in which persistent neutropenic fever triggers the addition of an antifungal agent, remains a common practice. However, the development of fungal diagnostic markers (e.g. galactomannan and β-glucan assays) combined with radiologic imaging has given potential to more targeted preemptive antifungal strategies.With the validation of preemptive strategies in clinical trials, we will likely have evidence-based targeted use of antifungals. PCR-based techniques are also promising tools for preemptive strategies and are undergoing evaluation. Knowledge of host genetic factors may be important in stratifying the risk for fungal disease during periods of high risk.