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Identification of fungi in tissue sections can be difficult. In particular, species of Aspergillus, Fusarium, and Pseudallescheria all appear as septate, branched hyphae. However, their differentiation can have significant clinical implications, as the latter two groups are often resistant to commonly used antifungal agents. In situ hybridization may assist in rapidly distinguishing these organisms in the absence of available culture. Oligonucleotide DNA probes were directed against the 5S, 18S, or 28S rRNA sequences of three groups of fungi with a high degree of specificity for each. Probes were tested on 26 formalin-fixed, paraffin-embedded tissue specimens, each with culture-proven involvement by one of these organisms:Fusarium species, n = 12;Pseudallescheria boydii, n = 5;Aspergillus species, n = 9 (Aspergillus probe set validated in an earlier study). Accuracy of both ISH and morphology was compared with culture.Morphologic examination (GMS and PAS) showed a greater sensitivity in detecting fungi (100%) as compared with in situ hybridization (84.6%). When detected, however, DNA probes allowed definitive identification of organisms. While there was no ability to distinguish between the three groups of organisms by morphologic features, ISH probes showed 100% positive predictive value (PPV, 19/19 organisms identified correctly). No cross-reactivity was observed when the probes were tested against other genera (100% specificity). Furthermore, the use of ISH allowed the detection of mixed fungal infections involving multiple organism types in two cases, demonstrating another advantage over morphology. In situ hybridization, directed against rRNA sequences, provides a rapid and accurate technique for distinguishing commonly encountered, nonpigmented filamentous fungi in histologic sections. While less sensitive than morphology, ISH is highly accurate and may help to distinguish between organisms that have similar or identical morphologic features by light microscopy.