Immunocompromised patients are at risk of developing fungal infections. Over time, the incidence of fungal infections and the spectrum of causative organisms have changed. In addition, treatment strategies in this high-risk population have also changed. Traditional approaches (using polyene-based therapy and older azoles), including empirical treatment strategies, have evolved to include prophylaxis in populations at the greatest risk. These strategies, although effective against Candida species, have not really impacted infections caused by Aspergillus spp. With the recent approval of antifungal agents with demonstrated activity against Aspergillus and other mould infections, there is hope for better outcomes in the treatment of established infections. Several agents, with activity against Aspergillus, have been shown to be effective in the empirical setting. The role of these new antifungal agents in the prophylactic setting remains unknown at present, but the potential for reducing Aspergillus infections is promising and requires ongoing study. The other area of significant research in fungal infections has been the search for accurate, non-invasive, rapid diagnostic tests. Over the past year, several publications have indicated that early diagnosis is possible in immunocompromised patients. These new diagnostics have paved the way for a new strategy, called pre-emptive therapy, enabling infected patients to be identified at an earlier stage of infection. This strategy will permit targeted antifungal therapy in those at greatest risk, and will avoid unnecessary, potentially toxic therapy in those not infected. Validations of the various techniques show promise and are reviewed in this paper.