Gene expression profiling of beta-catenin, Cripto and Wnt3 mutant mouse embryos has been used to characterise the genetic networks that regulate early embryonic development. We have defined genes whose expression is regulated by beta-catenin during formation of the anteroposterior axis and the mesoderm, and have identified Cripto, which encodes a Nodal co-receptor, as a primary target of beta-catenin signals both in embryogenesis as well as in colon carcinoma cell lines and tissues. We have also defined groups of genes regulated by Wnt3/beta-catenin signalling during primitive streak and mesoderm formation. Our data assign a key role to beta-catenin upstream of two distinct gene expression programs during anteroposterior axis and mesoderm formation.