Among the serious complications associated with bone marrow transplantation are invasive fungal infections caused by organisms such as Candida and Aspergillus species and end-organ disease caused by cytomegalovirus (CMV). Successful prevention of these complications can have a significant impact on morbidity and mortality. The primary option for prophylaxis against fungal infections is fluconazole (Diflucan). Low doses of intravenous amphotericin B may be useful where there is a higher rate of aspergillosis. Itraconazole (Sporanox) and nasal amphotericin B are other options that have been less well studied. The development of fluconazole-resistant candidiasis may become problematic. Ganciclovir (Cytovene) is useful for the prevention of end-organ disease caused by CMV but carries a significant risk for neutropenia. New techniques for the early detection of CMV infection should allow prophylaxis to be targeted to patients at highest risk of developing CMV disease. It is critical to clearly define the risk factors for fungal and CMV disease in the individual patient in order to minimize adverse effects and provide the optimal prophylactic benefit.