Purpose: To compare heme oxygenase 2 (HO-2) enzyme levels detected by immunohistochemical staining methods in the cornea epithelium obtained from keratoconus patients and normal subjects. Materials and Methods: The keratoconus group included 69 eyes of 69 patients with keratoconus scheduled for cross-linking surgery. The control group included 52 eyes of 52 patients with refractive error scheduled for photorefractive keratectomy surgery. After a detailed ophthalmologic examination, corneal topographic maps of each patient were generated, and then the patients underwent surgery. The corneal epithelium was collected mechanically during the surgery, fixed with formalin, embedded in paraffin blocks, and sectioned by microtomes. HO-2 antibodies were applied to the samples for immunohistochemical evaluation. The intensity of the staining was identified as negative, weak, moderate or strong. The keratoconus group was classified as early (average keratometry (AvrK) <= 47 D), moderate (AvrK 47-55 D) and advanced keratoconus (AvrK >= 55 D). Finally, intergroup and intragroup comparison analyses were made statistically. Results: In the keratoconus group, 20 (29%) (14 weak and 6 moderate staining) of the 69 corneal epithelial specimens were identified with HO-2 expression. In the control group, 40 (76.9%) (16 moderate and 24 strong staining) of the 52 corneal epithelial specimens were identified with HO-2 expression. HO-2 expression in the corneal epithelial specimens was significantly less in the keratoconus group than in the control group (p < 0.001). There was no substantial difference among the keratoconus subgroups in terms of staining with the HO-2 antibody (p = 0.797). Conclusions: The HO-2 enzyme staining using immunohistochemical methods was at lower amounts in the keratoconic corneal epithelial cells as compared with normal corneal epithelial cells. The HO-2 enzyme may play a role in the etiopathogenesis of keratoconus.