infiltrates associated with epidemic keratoconjunctivitis on corneal densitometry and total corneal higher order aberrations (HOAs), and to compare these measurements with the data obtained from their fellow unaffected healthy eyes. Methods: This prospective cross-sectional study included those who had persistent subepithelial infiltrates in only the affected eyes for at least three months and clinically normal fellow unaffected eyes. Corneal densitometry was measured with the densitometry software of the Pentacam HR-Scheimpflug corneal topographer over a 12 mm diameter of cornea. Further, total corneal HOAs including coma (Z[1,3], Z[3,-1]), trefoil (Z[3], Z[3,-3]), spherical aberration, higher order root mean square (HO-RMS), and total RMS in the Zernike analysis were analysed by the same Pentacam HR device. Results: Forty-six eyes of 23 participants were analysed in this study. The mean corneal densitometry values were statistically significantly higher in all annular concentric areas (0–2, 2–6, 6–10, and 10–12 mm) of the anterior and central corneal layers in the eyes with subepithelial infiltrates when compared to normal fellow eyes (p < 0.05, for each one). Additionally, there were statistically significant differences between the eyes with subepithelial infiltrates and normal fellow eyes with regard to coma, trefoil, HO-RMS, and total RMS in the Zernike analysis (p < 0.05, for each one). Conclusion: This study quantitatively demonstrated that persistent corneal subepithelial infiltrates associated with epidemic keratoconjunctivitis decrease corneal transparency and corneal optical quality in affected eyes.