Detailed study of the ectoderm and mesoderm has led to increasingly refined understanding of molecular mechanisms that operate early in development to generate cellular diversity. More recently, a number of powerful studies have begun to characterize the molecular determinants of the endoderm, a germ layer previously neglected in developmental biology. Work in diverse model systems has converged on an integrated transcriptional and signaling pathway that serves to establish the vertebrate endoderm. A T-box transcription factor identified in Xenopus embryos, VegT, appears to function near the top of an endoderm-specifying transcriptional hierarchy. VegT activates and reinforces Nodal-related TGFbeta signaling and also induces expression of essential downstream transcriptional regulators, Mix-like paired-homeodomain and GATA factors. These proteins cooperate to regulate expression of a relay of HMG-box Sox-family transcription factors culminating with Sox 17, which may be an obligate mediator of vertebrate endoderm development. This review synthesizes findings in three vertebrate model organisms and discusses these genetic interactions in the context of the progressive acquisition of endodermal identity early in vertebrate development.