Congenital aniridiaCongenital Aniridia is a rare genetic disorder of disrupted normal eyeEye development. Heterozygous mutations in the PAX6 genePAX6 gene are the main cause of the disease, of which over 500 distinct mutations are known to exist and lead to aniridiaAniridia. Importantly, patients with aniridiaAniridia are susceptible to total loss of vision from progressive aniridiaAniridia-associated keratopathy (AAK), believed to be triggered by dysfunctional limbal epithelial stem cells and/or the limbal stem cellLimbal stem cells niche. In the corneaCornea of aniridiaAniridia patients, a neurotrophic deficit is also present, that is closely associated with corneal inflammationInflammation, neovascularization, and a chronic wound healing response. This chapter summarizes corneal phenotypePhenotype in aniridiaAniridia-associated keratopathy (AAK), including its early manifestations in relation to PAX6 mutational status (genotypeGenotype). Detailed corneal imaging using slit lampSlit lamp biomicroscopyBiomicroscopy, in vivo confocal microscopyIn vivo confocal microscopy (IVCM), and optical coherence tomography (OCT) are used to document phenotypic changes in the epithelial, neural, and immune cell status in relation to the genotypeGenotype and the phenotypic grading of AAK, which, as a progressive pathology, is sensitive to age.