Laboratory investigations of stems cells in regenerative medicine have generated considerable interest within recent years, however some of this excitement is yet to be matched in the clinical arena. Two fields that are well poised to make significant clinical impact in the coming years are those of cartilage and corneal regeneration. In the case of cornea, it is widely acknowledged that corneal epithelium is derived from an adult stem cell type resident within the cornea. These cells, known as limbal stem cells (LSCs), have been widely investigated for their ex-vivo culture and subsequent transplantation efficacy, with some techniques already enjoying limited clinical application. Thus far however, only preliminary evidence currently exists to suggest that there is a population of adult stem cells which gives rise to stromal keratocytes or to the corneal endothelium. A handful of reports have discussed studies in which non-LSC adult stem cells such as mesenchymal stems cells (MSCs) or embryonic stem cells (ESCs) are being applied to corneal regeneration. Though adult stem cells have been shown to exist in articular cartilage, they have proven elusive, which corroborates the limited ability of this tissue to self-repair. Rather, MSCs, ESCs as well as adipose-derived, periosteum-derived, muscle-derived and synovium-derived stem cells (ADCs, PDCs, MDCs and SDCs respectively) are being extensively explored for cartilage regeneration. This review discusses emerging trends in the applications of both adult and embryonic stem cells to cartilage and corneal regeneration, with an emphasis on those techniques that have been applied clinically or which show significant potential for clinical translation.