This case series describes the use of in vivo confocal microscopy in the diagnosis and treatment of mycotic keratitis in two owls (one Bubo scandiacus, one Strix varia) and one woodcock (Scolopax minor). Each bird was at increased risk of fungal infection due to recent injury or stress. Ophthalmic findings in all birds included blepharospasm, ocular discharge, ulcerative keratitis, white or yellow corneal plaques, and anterior uveitis. Fungal hyphae were identified in corneal samples from all three eyes examined cytologically and in all three eyes by using in vivo confocal microscopy. Aspergillus fumigatus was isolated from a corneal culture in one bird. Despite medical treatment, progressive ocular disease prompted enucleation in two birds. Fungal hyphae were detected by histopathology in one of the two enucleated eyes. In vivo confocal microscopy aided the diagnosis of fungal keratitis in all birds and was the only diagnostic method that allowed immediate, real-time quantification of the extent (area and depth) and severity of mycotic keratitis.