BACKGROUND: Fungal keratitis is a major blinding eye disease found throughout the world, particularly in developing countries. Given the recent increase in Fusarium keratitis infections in contact lens wearers owing to contact lens solutions, a warning was recently issued by the Food and Drug Administration, making it a public health concern in developed countries. OBJECTIVE: To show the advantages of in vivo confocal microscopy imaging using the Heidelberg Retina Tomograph II-Rostock Cornea Module (HRTII-RCM) in the early diagnosis of fungal keratitis. METHODS: HRTII-RCM confocal microscopy was performed on five patients presenting with fungal keratitis and on three donor corneas contaminated with Fusarium solani, Aspergillus fumigatus and Candida albicans. RESULTS: Direct microscopic evaluation of corneal smears and culture revealed the presence of F solani in four cases and C albicans in one case. HRTII-RCM examination of the infected patients and contaminated donor corneas revealed numerous high-contrast elements resembling Fusarium, Aspergillus hyphae or Candida pseudofilaments in the anterior stroma. CONCLUSION: HRTII-RCM in vivo confocal microscopy is a new, non-invasive and rapid technique for the early diagnosis of fungal keratitis, showing high-resolution images resembling fungal structures in the early phase of the disease.