Stem cell therapy and organ regeneration are therapeutic approaches that will, we suggest, become mainstream for the treatment of human disease. Endothelial cells, which line the luminal surface of every vessel in the body, are essential components in any organ regeneration programme. There are a number of potentially therapeutic endothelial cell types, including embryonic, adult progenitor and induced pluripotent stem cell-derived endothelial cells, as well as host vascular cells. The features (benefits as well as disadvantages) of each cell type that make them potentially useful in therapy are important to consider. The field of stem cell biology is well developed in terms of protocols for generating endothelium. However, where there is a distinct and urgent unmet need for knowledge concerning how the endothelial cells from these different sources function as endothelium and how susceptible they may be to inflammation and atherosclerosis. Furthermore, where stem cells have been used in clinical trials there is little commonality in protocols for deriving the cells (and thereby the specific phenotype of cells used), administering the cells, dosing the cells and/or in assessing efficacy attributed to the cells themselves. This review discusses these and other issues relating to stem cell-derived endothelial cells in cell therapy for cardiovascular disease.