The PluriSys project is aimed at increasing the fundamental knowledge of basic biological processes of cell pluripotency and differentiation by generating new holistic data on gene expression and epigenetic modifications associated with cell pluripotency. The project integrates the multidisciplinary excellence in Europe in cell biology, molecular biology and bioinformatics. It also builds on earlier efforts, as consortium partners are leading partners in several EU funded projects in these areas. The PluriSys project links for the first time research activities in different mammalian systems, including murine, porcine and bovine, and in different cell types, from pluripotent cells in pre-implantation embryos, through embryonic stem cells, to epiblast-derived stem cells. Novel bioinformatics approaches and tools will be developed to set common standards for data analyses among all consortium members and, at a wider scale, to provide an integrated data base matching the requirements of systems biologists. Training, education and outreach activities are structured to assure the maximum efficiency in developing and spreading the new standards and to increase the impact of the project for the European Health sector. The project integrates SME partners and academic institutions from 7 countries from all regions of the EU and will help to decrease the fragmentation of ERA. The main impact of the project is expected as integrating efforts in cell biology, cell therapy, molecular biology and bioinformatics for future applications of systems biology on the relevant questions of cell pluripotency and differentiation. Furthermore, the project is expected to yield pracically useful results, such as improved procedures for the derivation, maintenance and differentiation of pluripotent stem cell lines in mouse and large animals, with potential future applications in the fields of regenerative medicine and tissue engineering, and, beyond these areas, in pharmaceutical industry and