The aim of this study was to find a reliable method for the detection and identification of fungi in fungus balls of the maxillary sinus and to evaluate the spectrum of fungi in these samples. One hundred twelve samples were obtained from patients with histologically proven fungal infections; 81 samples were paraffinembedded tissue sections of the maxillary sinus. In 31 cases, sinus contents without paraffin embedding were sent for investigation. PCR amplification with universal fungal primers for 28S ribosomal DNA and amplicon identification by hybridization with species-specific probes for Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus glaucus, Pseudallescheria boydii, Candida albicans, and Candida glabrata were performed for all samples. Furthermore, PCR products were sequenced. Fresh samples were also cultivated. Fungal DNA was detected in all of the fresh samples but only in 71 paraffin-embedded tissue samples (87.7%). Sequence analysis was the most sensitive technique, as results could be obtained for 28 (90.3%) fresh samples by this method in comparison to 24 (77.4%) samples by hybridization and 16 (51.6%) samples by culture. However, sequence analysis delivered a result for only 36 (50.7%) of the paraffin-embedded specimens. Hybridization showed reliable results for A. fumigatus, which proved to be the most common agent in fungus balls of the maxillary sinus. Other Aspergillus species and other genera were rarely found.Aspergillus spp. is the most commonly reported cause of fungal sinusitis and fungus balls of the sinuses, followed by dematiaceous fungi (5). Since the viability of fungal elements in fungus balls is poor, fungi frequently fail to grow from hyphae-rich material obtained during surgery. Furthermore, other limitations, such as slow growth of many relevant fungi, delayed production, lack of characteristic fruiting bodies or macroconidia, special nutritional requirements of certain fungi, and similarities in macromorphology or micromorphology or both at the genus level, may prevent their detection and identification. Histopathology reveals matted, dense conglomerations of hyphae separated from, but adjacent to, the respiratory mucosa of the sinus. Distinct features such as fruiting bodies (e.g., Aspergillus heads) and characteristic conidia or spores are rarely produced in vivo; thus, exact identification at the species level by histopathology is rendered nearly impossible. This might be the reason why it is still unclear as to how many of these infections are actually caused by Aspergillus species and what species of other fungi are common causes of fungus balls of the maxillary sinus. To our knowledge, there exist no data concerning the epidemiology of fungus balls of the maxillary sinus in Europe.PCR is a sensitive method which can be used to detect viable as well as nonviable fungal pathogens. Several fungus-specific primers have been described. A variety of PCR protocols for human samples have also been published, including panfungal PCR ass...