Previous studies have shown that the corneal epithelial stem cells are located at the limbal basal layer. The limbal stem cells are regarded as the ultimate source for corneal epithelial cell proliferation and differentiation. This paper examines epithelial wound healing in rabbit corneas with partial limbal deficiency (PLD), which was created by the surgical removal of two-thirds of the limbal zone (superior and inferior). Four to eight months after PLD creation, all corneas appeared normal, without vascularization. The residual stem cell capacity then was challenged by two sizes of corneal epithelial debridement created with combined n-heptanol and mechanical scraping. In the first group, two consecutive 6-mm defects were created 1 month apart. After the first wounding, three of eight PLD corneas had delayed wound healing and two of the three had vascularization, as compared to controls (n = 7). After the second wounding, both controls (n = 7) and the remaining PLD (n = 5) corneas showed similar rapid healing. In the second group, a large defect of up to 1 mm within the limbus was created. Healing was completed in 25-40 days in PLD (n = 6) corneas, a more marked delay compared to the 10-12 days for controls (n = 6) (P = 0.001). In addition, all PLD corneas showed increased vascularization and had epithelium of the conjunctival phenotype, verified by the immunofluorescent staining positive to AM-3 monoclonal antibody but negative to AE-5 monoclonal antibody. Thus, a deficiency of limbal stem cells contributes to the triad of conjunctival epithelial ingrowth, corneal vascularization, and delayed healing with recurrent erosion. In PLD, corneal epithelium is still compromised, particularly when a large epithelial cell mass is removed.