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PURPOSE To investigate the long-term clinical outcomes and changes in crystalline lens transparency after accelerated (45 mW/cm2) transepithelial corneal cross-linking (ATE-CXL) using the Pentacam imaging system in patients with progressive keratoconus. METHODS The study prospectively included 44 keratoconus eyes of 40 patients (mean age: 24.39  ±  5.61 years) who underwent ATE-CXL. The examinations, including assessment of uncorrected distance visual acuity, corrected distance visual acuity, corneal topography, and corneal endothelial cell density count, were conducted preoperatively and 1 month, 3 months, 6 months, 1 year, and 5 years postoperatively. Measurement of crystalline lens density using Pentacam images was also performed pre- and postoperatively. RESULTS All surgeries were uneventful with no postoperative complications. All keratometry values and corneal thickness remained stable during the 5-year follow-up period (all p > 0.05). There were no significant differences in corneal endothelial cell density count, visual acuity, and anterior average lens density in the 0.5-, 1.0-, and 1.5-mm depth zones during the 5-year follow-up period compared with the preoperative values (all p > 0.05). CONCLUSION The results of this study suggest that ATE-CXL at 45 mW/cm2 is safe and effective for the treatment of progressive keratoconus in terms of both crystalline lens density and endothelial cell density.