In immunocompromised patients suffering from invasive fungal infection, rapid identification of the fungal species is a prerequisite for selection of the most appropriate antifungal treatment. We present an assay permitting reliable identification of a wide range of clinically relevant fungal pathogens based on the highthroughput Luminex microbead hybridization technology. The internal transcribed spacer (ITS2) region, which is highly variable among genomes of individual fungal species, was used to generate oligonucleotide hybridization probes for specific identification. The spectrum of pathogenic fungi covered by the assay includes the most commonly occurring species of the genera Aspergillus and Candida and a number of important emerging fungi, such as Cryptococcus, Fusarium, Trichosporon, Mucor, Rhizopus, Penicillium, Absidia, and Acremonium. Up to three different probes are employed for the detection of each fungal species. The redundancy in the design of the assay should ensure unambiguous fungus identification even in the presence of mutations in individual target regions. The current set of hybridization oligonucleotides includes 75 speciesand genus-specific probes which had been carefully tested for specificity by repeated analysis of multiple reference strains. To provide adequate sensitivity for clinical application, the assay includes amplification of the ITS2 region by a seminested PCR approach prior to hybridization of the amplicons to the probe panel using the Luminex technology. A variety of fungal pathogens were successfully identified in clinical specimens that included peripheral blood, samples from biopsies of pulmonary infiltrations, and bronchotracheal secretions derived from patients with documented invasive fungal infections. Our observations demonstrate that the Luminex-based technology presented permits rapid and reliable identification of fungal species and may therefore be instrumental in routine clinical diagnostics.Although the vast majority of invasive fungal infections are still caused by Aspergillus or Candida species, changes in epidemiology have become evident over the last years (11,15,33,39). In view of the different drug resistance profiles of many clinically relevant fungal pathogens (34), the development of rapid methods for species-specific identification of clinically important fungi is desirable in order to permit selection of the most appropriate antifungal treatment. Traditional diagnostic approaches to the identification of fungal species are mainly based on phenotype analysis of fungal cultures. However, these approaches are time-consuming and show limited applicability for the detection of molds (29). Over the last years, a variety of molecular methods have been established for rapid and sensitive detection of fungal pathogens. Many of these assays are real-time quantitative PCR tests, mostly targeting the ribosomal multicopy gene (rDNA gene) (1, 3, 12-14, 16, 21, 30, 31, 35, 40). With these techniques, the fungal sequences of interest can be amplified by universa...