Studies on stem cells (SC) show that SC functions are determined by the extracellular microenvironment, known as the "niche", and by intrinsic genetic programs in the SCs; both are involved in regulating the delicate balance of self-renewal and differentiation. We have identified an animal model of limbal SC (LSC) deficiency and transplantation of SC-containing limbal tissue to treat the LSC deficiency, which could not only replace LSCs by providing new healthy corneal epithelial cells but also restore the lost niche of the limbal stromal layer, causing the regression of vessels and rearrangement of the corneal stromal lamellae. The purpose of the ex-vivo expansion technique is to develop a method that will enable culture of a small number of SCs which could than be expanded in a defined cultured system while preserving the original characteristics and properties of the SCs. In addition, SC characteristics will continue to be maintained when the cultured cells are transplanted back into the host. Bromodeoxyuridine-retaining, ΔNp63, ABCG2, p120, and N-cadherin immunoreactive studies of LSC cultured on an amniotic membrane have been performed. Pathological studies have been conducted for cases with preexisting central corneal stromal opacity treated by transplantation of LSCs followed by penetrating keratoplasty. The results indicate that the amniotic membrane can provide the niche environment for cultured LSCs and maintain the limbal-like environment for the transplanted area of cornea.