Phosphorylation of histone H2AX (cH2AX) is known to be the earliest indicator of DNA double-strand breaks. Recently, it has been shown that mouse embryonic stem cells (mESCs) have very high basal levels of cH2AX, even when they have not been exposed to genotoxic agents. As the specialized role of high basal cH2AX levels in pluripotent stem cells is still debated, we investigated whether H2AX phosphorylation is important in maintaining selfrenewal of these cells. Here, we report that not only mESCs but also mouse-induced pluripotent stem cells (miPSCs), have high basal levels of cH2AX. We show that basal cH2AX levels decrease upon ESC and iPSC differentiation and increase when the cells are treated with selfrenewal-enhancing small molecules. We observe that selfrenewal activity is highly compromised in H2AX2/2 cells and that it can be restored in these cells through reconstitution with a wild-type, but not a phospho-mutated, H2AX construct. Taken together, our findings suggest a novel function of H2AX that expands the knowledge of this histone variant beyond its role in DNA damage and into a new specialized biological function in mouse pluripotent stem cells.