The authors describe two cases of chronic ocular surface disorder caused by the use of soft contact lenses. These cases demonstrated persistent corneal epithelial abnormalities, indolent ulceration, superficial stromal scarring, peripheral vascularization, and decreased visual acuity (worse than 20/400). Both cases were refractory to medical management, including discontinuation of contact lenses and topical medications. Autologous conjunctival transplantation restored the ocular surface with the return of good visual acuity (better than 20/40). Tissue culture demonstrated a decreased replication rate in the limbal epithelial cells, which suggests that epithelial stem cell dysfunction may be responsible for this ocular surface disease.