There is an evolution in the demands of modern ophthalmology from descriptive findings to assessment of cellular level changes by using in vivo confocal microscopy. Confocal microscopy, by producing grey-scale images, enables a microstructural insight into the in vivo cornea in both health and disease, including epithelial changes, stromal degenerative or dystrophic diseases, endothelial pathologies, and corneal deposits and infections. Ophthalmologists use acquired confocal corneal images to identify health and disease states and then to diagnose which type of disease is affecting the cornea. This paper presents the main features of the healthy confocal corneal layers, and reviews the most common corneal diseases. It identifies the visual signature of each disease in the affected layer and extracts the main features of this disease in terms of intensity, certain regular shapes with both their size and diffusion, and some specific region of interest. These features will lead towards the development of a complete automatic corneal diagnostic system which predicts abnormalities in the confocal corneal data sets.