Purpose. To evaluate corneal thickness changes during pulsed accelerated corneal cross-linking (CXL) for keratoconus using a new isotonic riboflavin formula. Methods. In this prospective, interventional, clinical study patients with grades 1-2 keratoconus (Amsler-Krumeich classification) underwent pulsed accelerated (30 mW/cm(2)) CXL after application of an isotonic riboflavin solution (0.1%) with HPMC for 10 minutes. Central corneal thickness (CCT) measurements were taken using ultrasound pachymetry before and after epithelial removal, after riboflavin soaking, and immediately after completion of UVA treatment. Results. Twenty eyes of 11 patients (4 males, 7 females) were enrolled. Mean patient age was 26 ± 3 (range from 18 to 30 years). No intraoperative or postoperative complications were observed in any of the patients. Mean CCT was 507 ± 35 μm (range: 559-459 μm) before and 475 ± 40 μm (range: 535-420 μm) after epithelial removal (P < 0.001). After 10 minutes of riboflavin instillation, there was a statistically significant decrease of CCT by 6.2% from 475 ± 40 μm (range: 535-420 μm) to 446 ± 31 μm (range: 508-400) (P < 0.005). There was no other statistically significant change of CCT during UVA irradiation. Conclusions. A significant decrease of corneal thickness was demonstrated during the isotonic riboflavin with HPMC application while there was no significant change during the pulsed accelerated UVA irradiation.