When the entire corneal epithelium of the rabbit is mechanically removed, the denuded corneal stroma is completely resurfaced in 5-10 days with cells of conjunctival origin. The conjunctival cells differ from the corneal epithelial cells both morphologically and biochemically; however, within approximately 6 weeks, the conjunctival cells are converted into functional cornea epithelial cells. Using high-resolution agarose-gel electrophoresis, we compared the soluble proteins from functional conjunctiva (CON), functional corneal epithelium (EPI), and 'regenerating' corneal epithelium at eight intervals ranging from 24 hr to 6 weeks post-scraping. Comparison of CON and EPI patterns shows nine major mobility classes of proteins that fall into three subgroups: A = anodal, B = intermediate, and C = cathodal. The nine major classes have marked similarity in distribution and mobility, which may account for the apparent ease with which CON can transform into EPI during regeneration. Electrophoretic patterns of soluble proteins from regenerating epithelium suggest that the regeneration process occurs in three distinct phases: 24-72 hr post-scraping is a period of de-differentiation, 72 hr to 1 week is a period of reorganization, and 1-6 weeks is a period of differentiation. Specific protein groups are identified that represent fast-transforming, slow-transforming, conjunctival-specific, and corneal-specific proteins. Certain of these protein groups can be associated with particular stages in the regenerative process.