Tbx1 is a member of the Tbox family of binding domain transcription factors. TBX1 maps within the region of chromosome 22q11 deleted in humans with DiGeorge syndrome (DGS), a common genetic disorder characterized by numerous physical manifestations including craniofacial and cardiac anomalies. Mice with homozygous null mutations in Tbx1 phenocopy this disorder and have defects including abnormal cranial ganglia formation and cardiac neural crest cell migration. These defects prompted us to investigate whether extrinsic vagus nerve or intrinsic enteric nervous system abnormalities are prevalent in the gastrointestinal tract of Tbx1 mutant mice.We used in situ hybridization for Ret, and immunohistochemical staining for neurofilament, HuC/D and βIII-tubulin to study cranial ganglia, vagus nerve, and enteric nervous system development in Tbx1 mutant and control mice.In Tbx1(-/-) embryos, cranial ganglia of the glossopharyngeal (IXth) and vagus (Xth) nerves were malformed and abnormally fused. In the gastrointestinal tract, the vagus nerves adjacent to the esophagus were severely hypoplastic and they did not extend beyond the gastro-esophageal junction nor project branches within the stomach wall, as was observed in Tbx1(+/+) mice.Although cranial ganglia morphology appeared normal in Tbx1(+/-) mice, these animals had a spectrum of stomach vagus innervation defects ranging from mild to severe. In all Tbx1 genotypes, the intrinsic enteric nervous system developed normally. The deficit in vagal innervation of the stomach in mice mutant for a gene implicated in DGS raises the possibility that similar defects may underlie a number of as yet unidentified/unreported congenital disorders affecting gastrointestinal function.