The development of regenerative medicine relies in part on the capacity of stem cells to differentiate into specialized cell types and reconstitute tissues and organs. The origin of the stem cells matters. While autologous cells were initially the preferred ones the need for "off the shelf" cells is becoming prevalent. These cells will be immediately available and they originate from young non diseased individuals. However their allogenicity can be viewed as a limitation to their use. Recent works including our own show that allogenicity of stem cell can be viewed as on one hand detrimental leading to their elimination and on the other hand beneficial through a paracrine effect that can induce a local tissue regenerative effect from endogenous stem cells. Also their immune modulatory capacity can be harnessed to favor regeneration. Therefore the immune phenotype of stem cells is an important criteria to be considered before their clinical use. Immuno monitoring of the consequences of their in vivo injection needs to be taken into account. Transplantation immunology knowledge will be instrumental to enable the development of safe personalized regenerative stem cell therapy.