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To compare the effect of 2 different methods of transepithelial corneal collagen cross-linking (CXL) on corneal histology and hysteresis.The right eyes of New Zealand white rabbits (n = 50) were treated using one of the 2 transepithelial CXL methods. The eyes were then divided into 2 groups: group 1, transepithelial CXL using continuous ultraviolet A (UVA); group 2, accelerated transepithelial CXL using pulsed UVA.Both groups showed a postoperative increase in central corneal thickness. In both groups, an increase in corneal hysteresis was found after CXL, but the changes were not significant when compared with the baseline value. The corneal resistance factor and corneal-compensated intraocular pressure also remained unchanged in both groups after treatment. In both groups, the CXL effect reached the anterior–mid part of the corneal stroma. In group 1, CXL mostly affected the anterior–mid part stroma, whereas group 2 showed stromal keratocyte loss, and an acellular zone, in the deep stroma. More signs of keratocyte apoptosis were observed in group 2 than in group 1.Accelerated transepithelial CXL using pulsed UVA showed considerably deeper effect in the stroma with keratocyte loss than transepithelial CXL using continuous UVA.