In vivo confocal microscopy (IVCM) is a relatively new ocular imaging technique that permits morphological and quantitative assessment of the living cornea on the cellular level. The applications for IVCM in clinical ophthalmology are numerous and diverse. There are several advantages inherent to IVCM over standard diagnostic techniques currently used to confirm a diagnosis of infectious keratitis in veterinary ophthalmology. With IVCM, images can be viewed in real-time providing immediate diagnostic information. Traumatic corneal sampling techniques are avoided, and the procedure can be repeated as frequently as is clinically indicated without risk of corneal tissue damage. Both superficial and deep corneal lesions can be evaluated by IVCM in an atraumatic fashion.Microorganism viability is not required for their detection and specialized diagnostic laboratory assay procedures are not necessary. Many larger infectious agents can be directly identified within corneal lesions by IVCM, including fungi and parasites such as Acanthamoeba spp. In other situations, such as bacterial infectious crystalline keratopathy, the biological systems associated with the microorganism can be detected within the cornea. The current resolution of IVCM is inadequate to directly visualize some corneal infectious agents, such as herpesviruses, but host responses and virus-infected epithelial cells can be identified. This review summarizes the current knowledge and applications of IVCM in the management of infectious keratitis in veterinary ophthalmology, including its use in animals with bacterial, fungal, parasitic, and viral keratitis.