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Corneal cross-linking for the treatment of keratoconus has been tested in animal trials and proven clinically. A combination of in vivo confocal laser scanning microscopy (CLSM) and histology was used in rabbit corneas to assess early modifications at the cellular level after corneal cross-linking.Twelve New Zealand male rabbits were tested; in each case, the right eye was the study eye and left eye was the control eye. In vivo CLSM was performed on both eyes before and at 3 days and 1 week after cross-linking. Keratocyte and endothelial cell densities were determined by CLSM before and after cross-linking. After CLSM, the corneas were excised and processed for histology and immunohistochemistry.Massive edema was observed 3 days after cross-linking. The corneal epithelium had already closed again by day 3. No cellular structures were detected in the stroma and endothelium. One week after cross-linking, normal corneal transparency and thickness were restored. The anterior stroma still lacked nuclei. The number of nuclei in the posterior stroma was significantly lower than that in the intact corneas. Highly reflective spindle-shaped structures were detected in the posterior stroma. The endothelial monolayer had closed again but still showed significantly decreased cell density. At 1 week after cross-linking, immunohistochemical staining revealed the presence of proliferating cells in the corneal epithelium, posterior stroma, and endothelium.The early response of the rabbit cornea to cross-linking was successfully characterized at the cellular level by in vivo CLSM and histology, and the results obtained with both techniques correlated positively.