The objective of this study was to compare the transformation of genus-specific rabbit bone marrow (BM)-derived MSCs into corneal epithelium with acellular AM and MSC transplantation. Alkaline burn-induced 3rd degree limbal deficiency was created in 24 female rabbit eyes (including the cornea and the limbus). Each eye was administered 1N NaOH for 60 s with the use of 12-mm ring, and was then flushed with isotonic NaCl. The 24 rabbit eyes were divided into 3 groups, as follows: Group 1 (n = 8) had placenta-derived acellular AM, group 2 (n = 8) received no additional treatment, and group 3 (n = 8) had MSC (embedded in amniotic membrane) transplanted into the cornea. Group 3 was divided into 2 subgroups. In subgroup 3a marked MSC with DAPI [4,6,diamidino-2-phenylindole]) were used, and the rabbits were euthanized 12 d after transplantation, and their corneal blocks were examined with immunofluorescence microscopy. Subgroup 3b rabbits were euthanized 2 months after transplantation, and subgroup 3b, group 1, group 2 corneal blocks were evaluated histopathologically and immunohistochemically. The results were evaluated statistically. Conjunctivalization in group 3 was less severe than in groups 1 and 2. MSCs facilitated and accelerated the regeneration process in group 3. DAPI-positive MSCs were observed in the corneal endothelium, as well as in the inner nuclear layer of the retina in subgroup 3a. Cellular and acellular AM used for transplantation acted as barrier that prevented corneal perforation. MSCs had a beneficial effect on the regeneration process, and DAPI-marked MSCs were observed both in retina and cornea.