We developed a comprehensive dataset that samples the mouse transcriptome every 6 hr, from gastrulation through organogenesis. We observe an abrupt increase in overall transcript diversity at the onset of organogenesis (e8.0); the genes that comprise these changes are preferentially clustered along chromosome 7 and contain a significant enrichment of Gli binding sites. Furthermore, we identify seven dominant patterns of gene expression during gastrulation and organogenesis. Genes clustered according to these seven patterns constitute distinct functional classes, including a cluster enriched for gastrulation and pluripotency genes, two clusters differentially regulating localization and ion metabolism, and three clusters involved in discrete aspects of organogenesis. The last cluster is defined by a dramatic transient decrease in the expression of genes that regulate RNA processing and the cell cycle. Drosophila homologs of these genes are also coordinately downregulated following gastrulation, suggesting that the combined function of these genes has been conserved during metazoan evolution.