Embryonic stem cells (ESCs) have the capacity to form all the tissues in the body and hence, directed differentiation of ESCs along specific lineages represents a means to generate therapeutically useful cell types. It has been postulated that, during in vitro differentiation, ES cells sequentially pass through similar developmental stages as cells in the embryo. The availability of reagents that identify these stages would facilitate the monitoring and optimization of ESC differentiation. One key stage, the development of endodermal and mesodermal precursors in the early embryo, is marked by the transient expression of the transcription factor, Mixl1 and the stem cell gene, Oct4. In order to identify corresponding cells during ESC differentiation, we generated monoclonal antibodies to the Mixl1 protein that robustly detected both mouse and human proteins. Intracellular flow cytometry was used to show that approximately 90% of differentiating mouse ESCs transiently co-expressed Oct4 and Mixl1 proteins and that a subset of differentiating human ES cells also coexpressed MIXL1 and OCT4 proteins. These experiments have demonstrated for the first time by protein expression that both human and mouse ESCs passed through developmental stages during in vitro differentiation that corresponded to those observed in early mammalian development. Furthermore, these studies confirmed that anti-Mixl1 antibodies are a valuable reagent for monitoring ESC differentiation and will facilitate the efficient generation of clinically relevant cell types.