Antifungal prophylaxis represents a significant advance in the management of patients at risk from fungal infections in a variety of settings. Identification of patients at the highest risk and the utilisation of safe and effective drugs maximises the benefits of prophylaxis. Situations in which antifungal prophylaxis has been shown to be useful are bone marrow transplantation, liver and lung transplantation, surgical and neonatal intensive care units, secondary prophylaxis of fungal infections associated with HIV and neutropenia associated haematological malignancies and their treatment. New antifungal agents, such as the echinocandins and the new azoles, are available and have a potential role in antifungal prophylaxis. Future studies should evaluate which strategy is more useful; prophylaxis or pre-emptive therapy.