Invasive aspergillosis remains the primary cause of death from infection following allogeneic stem cell transplantation. Most cases occur during the second or third month after transplantation, during graft-versus-host disease or immunosuppression. Strategies for management of these cases include the development of more effective antifungals for prophylaxis, the use of biological markers to improve the early diagnosis of aspergillosis, new approaches to transplantation to reduce the risk of infection, and the emerging area of targeted cellular therapy.