The understanding of vertebrate development has greatly benefited from the study of gastrulation in the Xenopus embryo. Over the years, the molecular dissection of the Spemann organizer has proven to be a very fruitful source for gene discovery. Here, we report a comprehensive screen of gene expression in the Xenopus gastrula using cDNA macroarrays. Nylon filters containing more than 72000 cDNAs from a gastrula stage library were hybridized with differential probes from embryos in which organizer induction had been inhibited by reducing Nodal-related or maternal beta-Catenin signaling. Combining the changes in gene expression levels caused by these two major signaling pathways in a single graph identified both known and novel dorsoventral regulated genes. The most highly enriched organizer-specific genes were the secreted molecules chordin and Xnr-3, followed by the transmembrane protein paraxial protocadherin (PAPC). Ventral-specific abundant cDNAs included S10-40-H5, members of the Hyaluronan synthase family, Xvent-2 and XFD2/FoxI1. A differential probe of dorsal and ventral lips identified many more organizer-specific cDNAs than the screens inhibiting Nodal-related and beta-Catenin signaling, suggesting that additional, as yet uncharacterized signaling pathways, contribute to organizer formation. Finally, extension of this approach to the blastula preorganizer signaling center identified the transcription factor pintallavis/FoxA2 as a new preorganizer component.