This paper describes the use of amniotic membrane in the reconstructive surgical repair of generalized keratomalacia, ankyloblepharon, and after fibrous histiocytoma removal in two dogs and a cat. Case 1 was an 11-year-old female Yorkshire terrier with severe bullous keratomalacia in the left eye (OS). A frozen canine amniotic membrane graft and a third eyelid flap were applied. At day 80 postoperatively, only a mild scar and corneal vascularization were present. Case 2 was a 4-year-old female Siamese cat with symblepharon of both eyes after rhinotracheitis. Resection of the conjunctiva and frozen canine amniotic membrane transplant were performed. One month later, there was a little corneal scarring and corneal vascularization. Case 3 was a 6-year-old female terrier with a scleral and corneal mass at the 11–12 o’clock position (OS). Resection of the mass and amniotic membrane transplantation were performed. The mass was a fibrous histiocytoma localized to the sclera and cornea. This eye healed with mild conjunctivalization and no pigmentation. Amniotic membrane transplantation can be used as a method of reconstruction of the ocular surface with good repair of the cornea and minimal scarring in small animals.