Implantation of human embryonic stem cells (hES), derived progenitors or mature cells derived from hES has great therapeutic potential for many diseases. If hES would come from genetically unrelated individuals, it would be probably rejected by the immune system of the recipient. Blood groups, MHC and minor antigens are the immunogenetic hurdles that have to be crossed for successful transplantation. Autologous transplantation with adult stem cells would be the best approach but several elements argue against this option. Classical immunosuppression, depleting antibody, induction of tolerance and stem cell banking are alternative methods that could be proposed to limit the risk of rejection.