The cornea is the protecting and refractive part of the eye essential for proper visual acuity. Limbal epithelial stem cells (LESC) are responsible for maintaining the homeostasis of the corneal epithelium. They reside in the limbal stem cell niche within the transition region between the cornea and the sclera, the so-called limbus. The characterization of the stem cell microenvironment in terms of molecular regulation and cytoarchitecture remains the area of intensive research. Recently, novel niche structures were proposed: limbal epithelial crypts (LEC), limbal crypts (LCs) and focal stromal projections (FSPs). To date, a variety of limbal stem cells markers have been suggested but no definitive one has been identified. Limbal stem cell deficiency (LSCD) is a pathologic condition caused by destruction or dysfunction of LESC. This state may occur in a number of hereditary and acquired diseases and lead to pain, reduced visual acuity, and even blindness. This review will briefly outline the current state of knowledge on limbal stem cells biology and the role of transplanted stem cells as potential tools in regeneration of the cornea.