To determine the direct contribution of the epithelium to the generation of complications using a phototherapeutic keratectomy model. A mouse model with a genetically labeled epithelium was used to determine whether any epithelium-derived cells persist in the stroma up to 1 month after surgery. Also, gross histology and macrophotography of excimer-ablated rabbit corneas were analyzed for evidence epithelial ingrowths into the stroma. Epithelium-derived cells were present in the wounded stroma 1 month after surgery. Micrographs taken during the first 4 days during healing evidenced epithelial invasion of the stroma in one and sometimes more locations in the same cornea. Gross histology also revealed that the epithelial invasions can result in complete delamination of stromal tissue and subsequent inclusion of the stromal material in the epithelium. The epithelial inclusions ultimately created a highly irregular corneal surface. Ectopic epithelia are a known complication of LASIK and LASIK-like procedures. The data presented here indicate that ectopic epithelia are also a complication of surface ablation techniques. The knowledge that these complications are present following surface ablations provides a new understanding of the biological response to surface ablation techniques and suggests new avenues of study to improve clinical outcomes of those for whom LASIK-based techniques are not an option.