Pulmonologists and intensivists often care for patients at risk for infections caused by both Aspergillus and Candida. Infection with either can lead to severe life-threatening disease, particularly in immunosuppressed patients, with mortality rates for invasive fungal disease often exceeding 30%. For both organisms, multiple diagnostic challenges remain while newer diagnostic modalities are being developed and tested. Fortunately, therapeutic paradigms are shifting, and clinicians have many new agents in their armamentarium for combating fungal infection. Given the rapidly changing literature in this broad area, it is imperative that physicians caring for immunosuppressed patients and for the critically ill remain abreast of this evolving field.