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AIM: The aim of the study is to report the results of conjunctival-limbal autograft (CLAU) transplantation and penetrating keratoplasty (PK) in eyes with limbal stem cell deficiency (LSCD) due to chemical or thermal injury. METHODS: Thirty-one eyes of the 31 patients, who had unilateral LSCD due to chemical or thermal injury, were included in the study. Bilaterally affected cases and LSCD due to Steven-Johnson syndrome and mucous membrane pemphigoid were excluded from the study. All patients underwent a complete ophthalmologic examination. The surgical procedures, postoperative complications, ocular surface status, and visual outcomes were noted. RESULTS: In the CLAU group, regular corneal epithelium and ambulatory vision (≤1.0 logarithm of the minimum angle of resolution [20/200]) were achieved in 81% of eyes, including 22 eyes (71%) that were assessed after a mean follow-up period of 58 months, respectively. The 5-year survival rate of corneal allograft was 33%, 4 ± 13.9 in the CLAU applied eyes. In addition, the corneal graft clarity maintenance rate was found to be higher in patients having ≥12 months duration between CLAU and PK, which is statistically significant (62% vs. 23%,P = 0.046). CONCLUSION: Waiting at least 1 year after CLAU transplantation to perform PK increases corneal clarity. Eyelid problems, even if the eyelids were reconstructed properly, remain a major risk factor for the development of the epithelial disorder in the early and late postoperative period in CLAU applied eyes. [ABSTRACT FROM AUTHOR]