During the past two decades opportunistic fungal infections have emerged as important causes of morbidity and mortality in patients with severe underlying illnesses and compromised host defenses. While Aspergillus and Candida spp. collectively account for the majority of these infections, recent epidemiological trends indicate a shift towards infections by Aspergillus spp., nonalbicans Candida spp., as well as previously uncommon opportunistic fungi. Apart from an expanding number of different Zygomycetes, previously uncommon hyaline filamentous fungi (such as Fusarium species, Acremonium species, Paecilomyces species, Pseudallescheria boydii, and Scedosporium prolificans), dematiaceous filamentous fungi (such as Bipolaris species, Cladophialophora bantiana, Dactylaria gallopava, Exophiala species, and Alternaria species) and yeast-like pathogens (such as Trichosporon species, Blastoschizomyces capitatus, Malassezia species, Rhodotorula rubra and others) are increasingly encountered as causing life threatening invasive infections that are often refractory to conventional therapies. On the basis of past and current trends, the spectrum of fungal pathogens will continue to evolve in the settings of an expanding population of immunocompromised hosts, selective antifungal pressures, and shifting conditions in hospitals and the environment. An expanded and refined drug arsenal, further elucidation of pathogenesis and resistance mechanisms, establishment of in vitro/in vivo correlations, incorporation of pharmacodynamics, combination- and immunotherapies offer hope for substantial progress in prevention and treatment.