The ectoderm of the pre-gastrula Xenopus embryo has previously been shown to be at least partially patterned along the dorsal-ventral axis. The early expression of the anti-neural homeodomain gene Dlx3 is localized to the ventral ectoderm by a mechanism that occurs prior to gastrulation and is independent of the Spemann organizer. The repression of Dlx3 is mediated by signaling though β-catenin, but is probably not dependent on the induction of the Xnr3 or chordin genes by β-catenin. We propose a model in which this early regulation of Dlx3 accounts for the pro-neural bias of dorsal ectoderm.