Stem cells hold great clinical potentials for regenerative medicine. Pluripotent stem cells can give rise to any adult cell type. However, pluripotent stem cells have risk of tumor formation and have limitations because of their growth properties. Despite their potentials for therapeutic application, pluripotent stem cells may not be the most suitable for manufacturing process. The derivation of multipotent adult progenitor cells (MAPCs) from rodent bone marrow suggested that these cell types have more amenable properties for manufacturing process than pluripotent stem cells. Especially, rat MAPCs (rMAPCs) can differentiate into multiple lineages including hepatocyte-like cells, β-cell like cells, and mesodermal cells. However, they are not pluripotent and have less risk of tumor formation than pluripotent stem cells. In addition, because MAPCs can be cultivated as single cells, they are less vulnerable than pluripotent stem cells for robust expansion for potential clinical application. Although rMAPCs were derived from rat bone marrow, they resemble the cells in primitive endoderm (PrE) of mouse embryos. Here I showed that a similar population of nascent PrE cells can be derived from pluripotent rat embryonic stem cells (rESCs) by culturing in rMAPC medium conditions, and term these cells converted (c)HypoSCs. Like rMAPCs, cHypoSCs can readily differentiate towards cells with hepatic and mesoderm features in vitro, and generate extraembryonic endoderm in vivo. Transcriptome analysis and mass cytometry further showed that cHypoSCs exhibit nascent PrE gene expression properties that are similar to those of rMAPCs. Cross-species meta-analysis with single-cell transcriptome data confirmed that cHypoSCs are similar to early PrE cells of the mouse blastocyst, while rodent ESCs are similar to early epiblast (EPI) cells. Along with this finding, transcriptome analysis of human in vivo PrE cells and EPI cells uncovered potential culture conditions to derive human nascent in vitro PrE cells from human pluripotent stem cells. We demonstrated the potential of differentiation capacity of human pluripotent stem cells to nascent PrE cells using the identified culture conditions. This study will elucidate the underlying mechanisms of PrE differentiation, and will facilitate the derivation of potentially suitable type of cells for therapeutic application.