We report a case of atypical bilateral endogenous mycotic endophthalmitis in an infant. A diagnostic vitrectomy was done on the left eye. Electron microscope examination of the vitreous demonstrated fungal mycelia. Intravenous treatment with amphotericin B seemed effective for treating the infection of the right eye, but a vitrectomy was necessary to prevent deprivation amblyopia and retinal traction, secondary to persistence of a dense vitreous membrane.