Purpose. The study and comparison of the corneal tissues condition after the standard corneal collagen cross-linking (CXL) and femto-cross-linking in experiment.Material and methods. The study used 9 male Chinchilla rabbits (18 eyes) weighing 2-3kg, which were divided into 3 groups depending on the type of surgical intervention: femtocross-linking, standard CXL and the control group where the femtolaser formation of pocket were performed without the crosslinking procedure. Rabbits were taken out of the experiment at 1 week, 1 and 3 months. The eyes were enucleated, cornea was excised using a 9.0mm trephine. The corneal discs were examined by the transmission electron microscope JEOL 1200 EX (Japan).Results. Analysis of microscopic pictures from the transmission electron microscopy after the femto-cross-linking and the standard CXL revealed an equal quantity of cross-links in collagen fibers. After the standard CXL the changes in the basal membrane and basal epithelial cells were visualized with signs of polymorphism and increased intercellular spaces.Conclusion. In the electron-microscopic images of ultrastructure in the corneal stroma the comparable changes were found in the standard group and femto-cross-linking that suggests an identical efficiency of both techniques. The detected changes in the basal membrane a week after the standard CXL suggests a traumatism of the stage of epithelium removal in contrast to an atraumatic formation of stromal pocket using the femtosecond laser