Aim: The aim of the study was to assess the morphological changes in animal corneas following local cross-linking (CXL). Materials and methods: Experimental comparative study included nine isolated porcine eyeballs (ex vivo group) and nine Chinchilla rabbits, one eye per animal (in vivo group). All the corneas in both groups were saturated with 0.1% riboflavin and corneal CXL was performed with Locolink device (Transkontakt, Russia), a system that allows to deliver ultraviolet (UV) radiation through a mask of any pattern. One half of each cornea was cross-linked and the other half remained intact. Three corneas of each group were irradiated according to the standard Dresden protocol with 3.0 mW/cm² for 30 minutes (5.4 J); yet, three corneas were irradiated in accelerated CXL mode I with 6.0 mW/cm² for 15 minutes (5.4 J), and yet, three corneas were treated in accelerated CXL mode II with 5.0 mW/cm² for 10 minutes (3.0 J). In the ex vivo group, the corneas of the whole isolated porcine eyeballs were examined with optical coherence tomography (OCT): The stromal demarcation line depth was evaluated by 10 different topographical points per image and the optical density of the corneal layers over the demarcation line was evaluated qualitatively as positive or negative. In the In vivo group, the rabbits were sacrificed 5 days after treatment, and their eyes were enucleated. Corneoscleral buttons were excised and subjected to histological and transmission electron microscopy (TEM) examination. Results: Ex vivo group: Ultrastructural examination and OCT imaging showed that the demarcation line was more superficial after accelerated CXL than after standard CXL. In vivo group. No histological change was detected in the intact area. The re-epithelialization was complete by 72 hours after the procedure. Ultrastructural and histological examination on day 5 following complete re-epithelialization of the cornea showed the presence of bridge-like chains forming cross-links between collagen fibrils in tangential sections. Keratocytes in irradiated zones were either in the state of apoptosis or were activated and produced newly formed collagen. Conclusion: The method of local CXL allows to accurately and selectively modify limited regions of the cornea leaving other areas intact. In the case of local irradiation of the cornea, UV structural changes occur only within the irradiated area. The optimal protocol for use in local CXL is the Dresden protocol.