Background: Although a series of reports on corneal fungal infection have been published, studies on pathogenic mechanisms and inflammation-associated cytokines remain limited. In this study, aqueous humor samples from fungal keratitis patients were collected to examine cytokine patterns and cellular profile for the pathogenesis of fungal keratitis. Methods: The aqueous humor samples were collected from ten patients with advanced stage fungal keratitis. Eight aqueous humor samples from patients with keratoconus or corneal dystrophy were taken as control. Approximately 100 mu l to 300 mu l of aqueous humor in each case were obtained for examination. The aqueous humor samples were centrifuged and the cells were stained and examined under optical microscope. Bacterial and fungal cultures were performed on the aqueous humor and corneal buttons of all patients. Cytokines related to inflammation including IL-1 beta, IL-6, IL-8, IL-10, TNF-alpha, and IFN-gamma were examined using multiplex bead-based Luminex liquid protein array systems. Results: Fungus infection was confirmed in these ten patients by smear stains and/or fungal cultures. Bacterial and fungal cultures revealed negative results in all aqueous humor specimens. Polymorphonuclear leukocytes were the predominant infiltrating cells in the aqueous humor of fungal keratitis. At the advanced stages of fungal keratitis, the levels of IL-1 beta, IL-6, IL-8, and IFN-gamma in the aqueous humor were significantly increased when compared with control (p< 0.01). The levels of IL-10 and TNF-alpha also showed an ascending trend but with no statistical significance. Conclusions: High concentration of IL-1 beta, IL-6, IL-8, and IFN-gamma in the aqueous humor was associated with fungal keratitis.