The rapidity of modern genomic/proteomic technologies has opened up new possibilities for the diagnosis of invasive fungal infections (IFIs). Diagnosis of yeast infections requires direct detection in blood cultures but ideally even earlier detection in blood (whole blood, serum) and from other clinical samples. A number of commercial systems employing multiplex real time PCR, multiplex tandem PCR, and PCR-magnetic bead technology, have been trialled or are being trialled but thus far their clinical value remains uncertain and their applicability in different populations has not yet been systematically evaluated. PCR assays have been developed to detect both Candida and Cryptococcus species. Direct detection of moulds in clinical samples is also problematic with the possible exception of detection of the pathogen in tissue biopsy specimens; the sensitivity, and positive predictive values of various molecular assays have been suboptimal. Screening for invasive aspergillosis by detection of Aspergillus DNA in blood has utility and prevents unnecessary empiric antifungal therapy, in early diagnosis in high risk haematology patients, particularly if they are not receiving mould active prophylaxis.