Purpose Analysis of microstructural alterations of corneal and limbal epithelial cells in healthy human corneas and in other ocular conditions. Patients and methods Unilateral eyes of three groups of subjects include healthy volunteers (G1, n = 5), contact lens wearers (G2, n = 5), and patients with dry eyes (G3, n = 5) were studied. Imaging of basal (BC) and intermediate (IC) epithelial cells from central cornea (CC), corneal limbus (CL) and scleral limbus (SL) was obtained by in vivo confocal microscopy (IVCM). An appropriate image analysis algorithm was used to quantify morphometric parameters including mean cell area, compactness, solidity, major and minor diameter, and maximum boundary distance. Results The morphometric parameters of BC and IC demonstrated no significant differences (P40.05) between groups. Comparison between three corneal locations (CC, CL, and SL) within the groups showed significant differences (Po0.05) with mean values of cell area, compactness, solidity, and major and minor diameter of BC that increase from CC to limbus. The BC were round and regular in the central cornea (Po0.05) compared with CL and SL. Conclusions IVCM enables high-quality confocal images from central corneal and limbal epithelium. This quantitative study demonstrated morphological differences in the basal and intermediate epithelium between limbus and central cornea, and found no differences between contact lens wearers, dry eyes, and normal subjects.