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Fortunately, fungal infections of the eye are somewhat rare. They can affect the clear window of the eye (the cornea) or the internal eye (the retina and vitreous humor). There are only a few medicines that are safe and effective in the treatment of a fungal infection of the eye. The selection of which medication, what dosage, and how long the treatment will require are complex decisions and will be determined by your eye doctor based on the identification of the specific fungus involved and the portion of the eye that is infected.