In mouse embryo, the early induction of the head region depends on signals from the anterior visceral endoderm (AVE) and the anterior primitive streak. Subsequently, node derivatives, including anterior definitive endoderm and axial mesendoderm, are thought to play a role in the maintenance and elaboration of anterior neural character. Foxa2 encodes a winged-helix transcription factor expressed in signaling centers required for head development, including the AVE, anterior primitive streak, anterior definitive endoderm, and axial mesendoderm. To address Foxa2 function during formation of the head, we used conditional mutants in which Foxa2 function is preserved in extraembryonic tissues during early embryonic stages and inactivated in embryonic tissues after the onset of gastrulation. In Foxa2 conditional mutants, the anterior neural plate and anterior definitive endoderm were initially specified. In contrast, the axial mesendoderm failed to differentiate. At later stages, specification of the anterior neural plate and anterior definitive endoderm was shown to be labile. As a result, head truncations were observed in Foxa2 conditional mutants. Our results therefore indicate that anterior definitive endoderm alone is not sufficient to maintain anterior head specification and that an interaction between the axial mesendoderm and the anterior definitive endoderm is required for proper specification of the endoderm. Foxa2 therefore plays an integral role in the formation of axial mesendoderm, which is required to maintain the specification of the forebrain and the anterior definitive endoderm.