The aim of this study is to describe the corneal changes in three unrelated patients with ectrodactyly-ectodermal dysplasia-cleft lip and palate (EEC) syndrome and review the literature on the possible etiology and clinical presentation of similar cases. Case 1 is an 18-year-old female with cleft lip and palate, syndactyly, and bilateral corneal pannus superiorly and inferiorly. She was initially diagnosed and treated as herpes simplex virus keratitis. Case 2 is a 3-year-old female born with cleft lip and palate, absent radial digits in both hands, and bilateral lacrimal stenosis. She developed progressive stromal scarring and neovascularization in both eyes. Her cornea perforated after developing infectious ulceration. Case 3 is a 49-year-old male with cleft palate, claw-hand deformities, absent meibomian glands and lacrimal duct, right ankyloblepharon, and a superior wedge-shaped opacity in the left cornea. The clinical findings demonstrated the different spectrum of keratopathy seen in patients with EEC. All patients were treated medically and without any surgical intervention. Limbal stem cell deficiency (LSCD) is presumed to be the cause in all three cases. Corneal changes in EEC can have variable presentation. LSCD seems to be the etiology of such keratopathy. Recurrent infection from lacrimal drainage obstruction and tear film instability are other risk factors for disease severity and progression.