Pluripotent stem cells such as embryonic stem (ES) and induced pluripotent stem (iPS) cells have attractive attention as a source of cells for use in therapeutic application. However, as the in vitro differentiation culture does not provide usefully positional information for cell type definition, this system definitely requires visible markers to identify and monitor the intermediates that present on the way of differentiation. We have been developing the cell surface markers against the various types of mesoderm in the ES cell culture. Using it, we have identified the intermediates of mesoderm and dissected their differentiation pathways in ES cell differentiation. The method described here could be useful for inducing and purifying mesoderm cells from iPS as well as ES cell cultures.