Rapid and histology stains available for fungal examination and identification7 25–30
| Stain | Use | Comments |
| Calcofluor/Blankophor white | Detection of all fungi | Rapid. Alone or in combination with 10–20% KOH. Need for fluorescence microscope at 420 nm |
| Fontana–Masson stain | Histological stain for melanin | Stains the cell wall of Cryptococcus neoformans. Especially useful for differentiation of capsule-deficient C neoformans. Confirmation of melanin in lightly pigmented cells of dematiaceous (dark coloured) fungi. Cell walls stain brown/black |
| Giemsa | Staining of bone marrow and peripheral blood smears or sputum and BAL | Useful for Histoplasma and Pneumocystis species identification |
| Grocott-Gomori methenamine silver stain (GMS) | Histological stain | Provides optimal contrast for the detection of fungi in tissue. Specific for fungal cell walls. Fungi stain black, dark brown or grey. Stains old and non-viable fungal elements most effectively. Erythrocytes can mimic yeasts |
| H&E | General purpose histological stain | Stains most fungi. Allows demonstration of host tissue reaction. Demonstrates natural pigment in dematiaceous fungi. Not a specific fungal stain and fungal elements are easily missed. Cartilage and calcium deposits dark blue, cytoplasm and other components shades of red |
| India ink | Negative staining. Especially useful in CSF | Rapid. Detection of Cryptococcus species (encapsulated) |
| KOH | Clearing of specimen to allow improved visibility of fungal elements. Mostly with solid specimens | Rapid. With or without incubation at 56°C. May produce artefacts due to crystallisation of the KOH especially on drying |
| Lactophenol | Lactophenol: preserves fungal structures and kills the fungus. Cotton blue: stains the fungal elements | Rapid. Clear and specific images of fungal elements. Mostly used at the identification steps |
| Lactophenol-cotton blue | ||
| Mayer's mucicarmine stain | Histological stain | Specifically stains mucopolysaccharide capsular material of several fungi. May help in confirmation of cryptococcal infection |
| Papanicolaou stain | Cytological stain mainly used to detect malignant cells | Stains most fungal elements |
| Periodic acid-Schiff stain | Histological stain | Stains yeasts and hyphae. Possible artefacts with yeasts. Fungi appear red-purple. Zygomycete hyphae may stain poorly |