A 22-year-old Indian female was referred to Sg Buloh hospital with the diagnosis of bilateral keratoconus. On examination, slit lamp biomicroscopy and corneal topography revealed stage 3 keratoconus in the right eye and stage 2 keratoconus in the left eye. Corneal cell morphology in both eyes was evaluated using confocal microscope. In qualitative observation, almost all corneal layers in right eye except endothelium were partially or completely obscured by haze. Additionally, morphological alterations, such as elongation of keratocyte nuclei and cluster of cells, and dark bands in the anterior stroma were observed in right eye. In the left eye, the amount of haze was less, allowing better visibility of the corneal layers compared with the right eye. The dark bands were evident in the posterior stroma. Quantitative analysis showed that anterior and posterior stromal keratocyte density and endothelium cell density were relatively low in the right eye (834.0, 700.5, and 2,133 cells/mm2, respectively) compared with the left eye (934.1, 750.6, and 2,361 cells/mm2, respectively). In this case, the right eye, exhibiting stage 3 keratoconus, showed more morphological alteration, particularly in the anterior stroma compared with the left eye with stage 2 keratoconus. Increased severity of the disease can explain these differences in corneal cell morphology.