Long-term preservation of corneal limbal epithelium may decrease its quality and change the molecular signature of the limbal epithelial stem cells. In this study we have investigated the molecular profile of isolated corneal epithelial cells that have been in storage for an extended time. Isolated cells were characterised by the expression profile of different cytokeratins and markers of squamous metaplasia (vimentin and α‑actin). Furthermore, we examined global markers of adult stem cells including p63α and ABCG2 but also Lgr5 as a novel stem cell marker. Immunocytochemical staining and PCR analysis of p63α, ABCG2 and Lgr5 revealed the existence of side-population cells with a stem-cell phenotype and maintenance of corneal limbal stem cell properties. Lgr5 expression can be related to cellular stemness and can be considered as a new phenotypic marker of residual human corneal limbal stem cells. However, the existence of ck10 together with co-expressed α-actin and vimentin suggests that the corneas investigated were under oxidative stress and showed evidence of squamous metaplasia.