Pluripotent stem cells were established from pre- and post-implantation embryos (ESC and EpiSC respectively). While all can differentiate in vitro into cells representative to the three germ layers, only ESCs can participate to chimeras. Moreover, mouse ESCs initially cultured in media containing serum and leukemia inhibitory factor (S/L) were found to be heterogeneous and exhibit fluctuating pluripotency states. However, when cultured in serum-free medium in the presence of two inhibitors (2iL) targeting MEK1/2 and GSK3α/β pathways, cells reach a homogeneous state called naïve ground state. Endogenous retroviruses (ERVs) are the hallmark of ancient retroviral integrations into genomes. Some ERVs are reactivated in early embryo development and their expression profile is specific to each ERV. The objective of this work is to decipher the reversion process from fluctuating pluripotency to homogeneous naïve ground states by exploiting ERV reactivation properties to label cells according to their pluripotency status and select cells with the highest chimeric potential. Methodology: Fluorescent reporter genes whose expression is controlled by ERV promoters were introduced into mESCs. The reversion of mESCs into the naïve ground state by transitioning from a S/L to a 2iL culture condition is followed by reporter gene expression analyses by flow cytometry. Endogenous gene transcriptions were evaluated overtime by RNAseq. Chimeric potential was assessed by microinjecting cells into embryo at the morulae stage and analyzing their colonization at blastocyst stage. Results: ERV reporters have highly specific expression profiles depending on cell culture conditions. We demonstrated that the reversion of mESCs into the naïve ground state by transitioning from S/L to 2iL condition takes several cell divisions and goes through several transient states including a 2C-like stage. Thanks to the activities of those ERV reporters, we were able to enrich populations with different transcriptional profiles, demonstrating variable abilities to participate in embryonic development when injected into mouse embryo. Conclusion: These ERVs derived reporters hold considerable potential for identifying and subsequently isolating cells based on their different pluripotency status, enabling us to decipher the different phases of cell reversion into naïve ground state. Altogether, those reporters could efficiently help isolate PSCs from the embryos with the desired pluripotency state.