Corneal lesions in aniridia include peripheral pannus and epithelial abnormalities that may advance centrally, resulting in the need for penetrating keratoplasty. Three patients with aniridia who underwent repeated corneal surgical procedures (one keratectomy and six penetrating keratoplasties) are described herein. A clinicopathological correlation was performed. In all three patients there was evidence of recurrent pannus and epitheliopathy on histopathological examination, which correlates with the clinical findings. These findings suggest that the pathophysiology of recurrent aniridia keratopathy may be related to a primary abnormality in the stem cells of the recipient corneal limbus. Aniridic pannus and epitheliopathy recur in grafts after penetrating keratoplasty and threaten the transplanted cornea. The risk of recurrent keratopathy should be considered when recommending a surgical procedure to patients with aniridia.