Invasive fungal infections remain an important cause of morbidity and mortality in transplant recipients. Since conventional diagnostic tools such as culture lack sensitivity and specificity, alternative diagnostic assays have been developed. Among the most promising techniques are the detection of fungal DNA and serology. Fungal DNA can be detected with high sensitivity and specificity when performed with specimens from sterile sites such as blood. Polymerase chain reaction (PCR) assays can be used to detect a broad range of fungal pathogens and combined with species identification. Multicenter diagnostic studies are needed to establish the diagnostic value of PCR but lack of standardization hampers such studies. The serodiagnosis of invasive fungal infections has become an important tool in the management of invasive fungal infections. Especially the detection of circulating galactomannan has been shown to be a sensitive marker for invasive aspergillosis. Both serology and PCR can be used to monitor the response to antifungal therapy. The optimal use of non-culture-based methods is in prospective screening of patients at high risk. Since the incidence of disease greatly influences the positive predictive value, screening should take place only in those patients at very high risk for invasive fungal disease.