Corneal blindness carries a morbidity that affects quality of life and is often associated with an increased economic burden. In this review, we focus on the severe and painful condition of limbal stem cell deficiency, an important cause of corneal blindness. Conventional corneal transplantation usually results in graft failure and is contraindicated in this condition. Ex vivo-expanded limbal epithelial transplantation has been used as a cellular-based therapy to regenerate and reconstruct the ocular surface as a mode of treatment. Enrichment methods for stem cells are a strategy to improve the outcome of limbal stem cell transplantation. Here we discuss the side population assay as a functional assay to enrich for stem cells as an important source of limbal stem cells. The challenges in ex vivo-expanded limbal stem cell transplantation are wide and varied and will be addressed in this review with regard to improving the clinical outcomes of cultivated limbal stem cell transplantation.