Infections remain a major complication of hematopoietic stem cell transplantation, with recent trends indicating that fungal pathogens have become one of the most common causes of death. Attention has turned to the use of prophylactic antifungal medications to prevent infection with bothCandidaandAspergillusspecies. Recent studies, which are reviewed within, indicate success in preventing infections caused by azole-susceptibleCandidaspecies, accompanied by improved transplant-related mortality rates in high-risk patients. Further studies are necessary to develop strategies to prevent infection withAspergillusspecies.