In recent years, invasive fungal infections have emerged as an increasing cause of morbidity and mortality in immunocom-promised patients. Early diagnosis of invasive fungal infections remains difficult as the currently available detection systems lack either sensitivity or specificity or both. Therefore, anti-fungal therapy is more often administered for clinically presumed than for proven fungal infection. Culture detection of fungal species from blood is not sensitive enough. Thus, assays for detection of fungal specific circulating antigens have been developed and applied in defined patient populations. Recently, polymerase chain reaction (PCR) assays have emerged as powerful tools with high sensitivity and specificity for the diagnosis of a broad variety of fungal pathogens. PCR has been applied successfully for detection of fungal pathogens in experimental settings, and encouraging preliminary results concerning application of PCR to clinical samples are available. Further prospective trials will help to define the potential clinical value of the new assays discussed.