Background Differentiated somatic cells can be reprogrammed in induced pluripotent stem cells (iPSCs); a cell type with great potentials in regenerative medicine and in vitro disease modeling. In the pig, we have developed iPSCs, but proper culture conditions for maintaining pluripotency over time are still lacking. Hence, there is a need for a more fundamental dissection of the pluripotency apparatus in the pig as well as in cattle. Objectives The aim of this study is to analyze RNA-seq data to increase the knowledge about biological pathways in porcine and bovine embryonic pluripotent cell populations exploiting the mouse data as proof of principle. In particular we studied cell populations from three different stages of pluripotency after fertilization: the inner cell mass, the epithelial epiblast and the gastrulating epiblast. Understanding the molecular basis of these states may allow for stable culture of pluripotent cells in pig and cattle. Methods After quality control reads were pre-processed and mapped with STAR aligner. Post-mapping quality was checked with Qualimap. Finally the expression levels were estimated using HTSeq. Gene co-expression will be analyzed using a weighted network based method to identify highly co-expressed genes (module) and hub genes. Modules with a potential role in pluripotency will be identified with enrichment procedure and regulator genes identified with LemonTree algorithm. Differential wiring of modules among species will be evaluated. Expected results We expect to find out candidate pluripotency factors in porcine and bovine embryo. Acknowledgements We thank for the financial support from the EU project PluriSys, HEALTH-2007-B-223485.