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Transplantation of the autologous cultured corneal limbal epithelium and oral mucosal epithelium is a standard technique for ocular surface reconstruction under corneal limbal stem cell deficiency. As an option for bilateral cases, we recommend utilization of autologous conjunctivae for ocular surface reconstruction. Autologous conjunctival epithelium sheet transplantation was effective for bilateral corneal limbal stem cell deficiency without symblepharon or severe keratinization. Moreover, we established a feeder-free and serum-free culture system of the limbal epithelium. This system can be applied for culturing conjunctival epithelia. Autologous cultured conjunctival epithelium transplantation is a practical option for treating bilateral corneal limbal stem cell deficiency.