Although a number of studies have been published on antifungal prophylaxis in neutropenic and bone marrow transplantation patients, there are a lot of conflicting data. Some of this may be due to a lack of consensus on the definition of fungal disease and the definition of end-points for treatment. The risk factors associated with fungal infection, the causative species and the antifungals currently used for prophylaxis are reviewed. Future trends in prophylaxis, such as the use of growth factors and peripheral blood stem cells are discussed.