Although the gut is homologous among different vertebrates, morphological differences exist between different species. The most obvious variation in the guts of extant vertebrates appears in the stomach. To investigate the evolution of this structure, we compared the histology of the stomach and gastrointestinal tract in amphibian (Xenopus laevis), avian (Gallus gallus), and mammalian (Mus musculus) organisms, and defined the expression patterns of several genes within the developing guts of these lineages. In all three groups, we find that the anterior portion of the stomach has a similar glandular histology as well as a common embryonic expression of the secreted factors Wnt5a and BMP-4. Likewise, within the amniote lineages, the posterior nonglandular stomach and pyloric sphincter regions are also comparable in both histological and molecular phenotypes. The posterior stomach expresses Six2, BMPR1B, and Barx1, whereas the pyloric sphincter expresses Nkx2.5. Although the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates, the histology of the Xenopus tadpole gut shows less distinct variation in differentiation in this region, which is most likely a derived condition. The molecular signature of the embryonic Xenopus gut correlates with the more derived morphology of the larval phase. We conclude that the global patterning of the gut is remarkably similar among the different vertebrate lineages. The distinct compartments of gene expression that we find in the gut be necessary for the unique morphological specializations that distinguish the stomachs from terrestrial vertebrates.