Corneal blindness is a leading cause of vision loss globally. From a tissue engineering perspective, the cornea represents specific challenges in respect to isolating, stably expanding, banking, and effectively manipulating the various cell types required for effective corneal regeneration. The current research trend in this area focuses on a combined stem cell component with a biological or synthetic carrier or engineering scaffold. Corneal derived stem cells play an important role in such strategies as they represent an available supply of cells with specific abilities to further generate corneal cells in the long term. This chapter describes the isolation protocols of the epithelial stromal and endothelial stem cell populations.