The purpose of this study was to identify the in vivo microstructural characteristics of an animal model of 'epithelialization of the endothelium' that are similar in appearance to the in vivo confocal microscopical appearance of corneal endothelium previously thought to be diagnostic of irido-corneal endothelial syndrome, and correlate these observations with ex vivo in situ confocal microscopical analysis. A rat model (n = 8 eyes)of transient 'epithelialization of the endothelium' resulting from superficial corneal trauma, was developed and analysed using in vivo confocal microscopy. One animal was killed at 48 hand the cornea was immuno-labelled and analysed, using ex vivo in situ confocal digital image reconstruction. Reversible 'epithelialization of the endothelium' was observed by in vivo confocal microscopy 48 h after superficial corneal trauma in all eight eyes. Ex vivo in situ analysis failed to demonstrate immunohistological characteristics of epithelialization. In vivo confocal microscopy is based on optical principles, and as a result various structural alterations may present with apparently identical characteristics that should be interpreted cautiously, on the basis of the presented clinicopathological observations.