Invasive fungal infections account for significant morbidity and mortality in the seriously immunocompromised host, especially those suffering from hematologic malignancies and the recipients of hematopoietic cell transplant. One of the reasons for the continuing high mortality rates due to invasive fungal infection is the delay in administering appropriate therapy. As preemptive antifungal therapy is not feasible for lack of a predictive test, early empiric therapy is currently the only approach likely to result in improvement in survival. Here, we present our approach to both invasive candidiasis and invasive mold infection. Therapy should be initiated at the first signs and symptoms of disease, utilizing knowledge of local fungal epidemiology, the patient's recent antifungal agent exposure, and the diagnostic tests immediately available, to select an appropriate antifungal agent most likely to be effective against the suspected fungal species.