Summary: Forty projects on stem cell research, tissue and matrix engineering, tolerance induction and other topics were supported by the Swiss National Research Program NRP46 (Implants, Transplants) from 1999 - 2006. The last project is devoted to developing stem cell lines from frozen surplus human embryos in Switzerland, which would otherwise have to be destroyed at the end of 2008. It is entitled JESP (Joint Embryonic Stem Cell Project) since it involves two Swiss universities, in vitro fertilisation centres and experts from the humanities (ethics and law) to handle this difficult problem. Over the years, stem cell transplantation and tissue/matrix engineering have drawn closer to each other and even developed synergies. Progress in stem cell research has been slower than anticipated, but a multitude of technical skills (phenotyping, isolation, transfection, induction of differentiation, labeling, expanding cells in culture, etc) were acquired. Understanding of stem cell biology has grown. The 7 projects on tissue and matrix engineering progressed closer to clinical applicability than the stem cell projects. Of 3 projects to implant encapsulated cells for the production of hormones (insulin, erythropoietin), one is close to clinical pilot studies with an advanced encapsulated device. Five projects were devoted to mechanisms of tolerance or the role of metzincins in chronic allograft nephropathy. Four studies in psychology and communication in transplantation were funded, as were 5 projects in ethics, law and the history of transplantation in Switzerland. The goal of NRP46 was to provide an impulse for research in these new fields and bring together experts from the humanities, biology and medicine to cope more effectively with the problems of regenerative medicine in the future. The majority of goals were attained, mainly in the basics.