Background: The contribution of the endoderm to the oral tissues of the head has been debated for many years. With the arrival of Cre/LoxP technology endoderm progenitor cells can now be genetically labeled and tissues derived from the endoderm traced. Using Sox17-2A-iCre/Rosa26 reporter mice we have followed the fate of the endoderm in the teeth, glands, and taste papillae of the oral cavity. Results: No contribution of the endoderm was observed at any stage of tooth development, or in development of the major salivary glands, in the reporter mouse during development. In contrast, the minor mucous glands of the tongue were found to be of endodermal origin, along with the circumvallate papilla and foliate papillae. The mucous minor salivary glands of the palate, however, were of mixed ectodermal and endodermal origin. Conclusions: In contrast to urodele studies, the epithelium of murine teeth is derived solely from the ectoderm. The border between the ectoderm- and endoderm-derived epithelium may play a role in determining the position of the lingual glands and taste buds, and may explain differences observed between taste buds in the anterior and posterior part of the tongue.