Dimorphic fungal infections (histoplasmosis, blastomycosis, coccidioidomycosis, and cryptococcosis) can occur in immunocompromised and healthy individuals. Cutaneous involvement is often secondary and may be the presenting sign of systemic disease. These ominous infections are frequently clinically indistinct, and patient prognosis is influenced by a timely diagnosis and treatment. Morphologic differentiation between these organisms is not definitive, and tissue cultures represent the diagnostic gold standard in current day practice. However, tissue cultures are rarely obtained and merely represent an afterthought in seemingly unsuspecting cases. Furthermore, when performed, they may take several days or weeks for completion. In situ hybridization (ISH) utilizing oligonucleotide probes directed against fungal ribosomal RNA is a rapid and accurate assay for the identification of dimorphic fungi in paraffin-embedded tissue sections. We present five patients in whom ISH both prospectively and retrospectively confirmed the presence of a cutaneous infection (histoplasmosis, blastomycosis, coccidioidomycosis, and cryptococcosis). In all of the skin sections analyzed, dimorphic fungi were morphologically apparent but not diagnostically discernible. In summary, ISH is a valuable tool in the prompt diagnosis of cutaneous deep fungal infections.