Fungal infections are currently a leading cause of infectious morbidity and mortality in patients undergoing allogeneic blood and marrow transplantation (BMT). Although the introduction of azole antifungals for prophylaxis has had a significant impact on the incidence of candidal infections (especially those caused by C. albicans and C. tropicalis), invasive aspergillosis has increased in incidence in many centers worldwide. Given the long risk period corresponding with graft-versus-host disease, and the toxicities of currently available mold-active antifungals, the development of a prevention strategy for these angioinvasive molds remains a challenge. The introduction of new antifungal drugs and adjunctive therapy to improve immune function may be beneficial in decreasing mortality associated with these infections in the future. Most importantly, a greater understanding of the pathogenesis of fungal disease and specific host risks is necessary to impact this increasingly important infection in immunocompromised hosts.