Despite the increasing importance of nosocomial fungal infections, very little is known of the epidemiology, mode of transmission, or pathogenesis of infections due to fungal pathogens. Recently, a number of potentially useful epidemiological typing systems have been employed for identification of strains within species of Candida and other fungi. Epidemiological studies employing either DNA-based or protein-based typing methods have provided some interesting insights into the epidemiology of nosocomial fungal infections, particularly nosocomial candidiasis. Careful epidemiological studies employing selected typing methods are essential to the rational development of effective measures for prevention and control of nosocomial infections caused by opportunistic fungal pathogens.