AIM: To determine typical corneal changes of congenital aniridic keratopathy (CAK) using corneal topography and confocal systems, and to identify characteristics that might assist in early diagnosis. METHODS: Patients with CAK and healthy control subjects underwent detailed ophthalmic examinations including axial length, corneal thickness, tear film condition, corneal topography, and laser-scanning in vivo confocal microscopy (IVCM). RESULTS: In early stage aniridic keratopathy, Schirmer I test (SIT), break-up time (BUT), mean keratometry (mean K) and simulated keratometry (sim K) were reduced relative to controls (P<0.05), while simulation of corneal astigmatism (sim A) and corneal thickness were increased (P<0.05). In addition, significantly more eyes exhibited flat cornea compared with the control group. Inflammatory dendritic cells were present in the aniridic epithelium, with significantly increased density relative to controls (P<0.05). Palisade ridge-like features and abnormal cell morphology were observed in six out of sixteen CAK cases. In central cornea area, the aniridic corneas had the increased subbasal nerve density. CONCLUSION: These changes in corneal morphology in borderline situations can be useful to confirm the diagnosis of CAK.