Purpose.To report three cases of limbal stem cell deficiency (confirmed by impression cytology) that followed multiple pterygium surgeries and therapeutic penetrating keratoplasty.Methods.The first case, after multiple pterygium surgeries, presented with corneal scarring and thickened epithelium with vascularization sparing the central cornea in the right eye and involving the entire cornea in the left eye. The second case presented with superficial scarring and extensive vascularization after failed therapeutic graft performed for a large perforated corneal ulcer. The third case was a clear graft performed for a progressing fungal ulcer with signs of conjunctivalization inferotemporally. Limbal stem cell deficiency was clinically suspected in all of these cases.Results.Goblet cells with mucin globules were found on the corneal surface by impression cytology in all three cases.Conclusions.We report three cases of limbal stem cell deficiency (proven by impression cytology) that followed multiple pterygium surgeries and therapeutic penetrating keratoplasty. Surgical insult to the limbus is the predisposing factor for stem cell damage in these cases. Involvement of the limbus by infection and use of intensive medications are probable contributing factors for stem cell damage in cases of therapeutic penetrating keratoplasty.