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In this study, we investigated the effect of photodynamic therapy (PDT) on the healing of corneal alkali burns in rats. The experiment was performed on 50 adult non-linear rats. Depending on the intervention, the animals were divided into 5 equal groups with 10 animals in each group: Group 1 included rats with intact eyes (the control group) and Groups 2 through 5 were experimental groups with EAB. Group 2 consisted of rats subjected to instillation of 0.25% chloramphenicol solution; Group 3 consisted of rats subjected to photodynamic irradiation according to our scheme: 300 mJ (630 nm) for 3 minutes; Group 4 consisted of rats subjected to instillation of methylene blue (MB); Group 5 consisted of rats subjected to instillation of MB with subsequent photodynamic irradiation according to the described scheme. During all periods of observation, the infiltration of the subcorneal zone was less pronounced in Group 5 than in the other groups and was represented mainly by round cells in the anterior chamber, iris, retina, and ciliary zone. The instillation of MB with subsequent photodynamic irradiation was the most effective in reducing the bacterial contamination Thus, PDT with the photosensitizer methylene blue, in accordance with the designed exposure mode, provided the epithelialization and bacteriostatic effect during corneal repair after EAB. In conclusion, PDT improves a wound’s healing process, which is expressed in the reduction of inflammatory infiltration and the promotion of corneal epithelialization.