We have determined whether brain-derived neurotrophic factor immunoreactive (BDNF-ir) neurons in the vagal ganglia innervate the gastrointestinal tract. Many BDNF-ir neurons were medium in size and located throughout the jugular and nodose ganglia. When Fluorogold was injected into the wall of the cervical esophagus, many retrogradely Fluorogold-labeled neurons were found in both the jugular ganglion and the nodose ganglion. When Fluorogold was injected into the body of the stomach or applied to the cut end of the subdiaphragmatic vagus nerve, numerous Fluorogold-labeled neurons were found mostly in the nodose ganglion. Double-labeling combining immunohistochemistry for BDNF and retrograde tracing with Fluorogold showed that more than 90% of the neurons in the jugular ganglion and the nodose ganglion projecting to the cervical esophagus contained BDNF-like immunoreactivity. In the cases of both Fluorogold injection into the stomach and Fluorogold application to the subdiaphragmatic vagus nerve, almost all Fluorogold-labeled neurons in the nodose ganglion contained BDNF-like immunoreactivity. These results indicated that almost all vagal sensory neurons located in either the jugular ganglion or the nodose ganglion that innervate the gastrointestinal tract are BDNF-ir neurons.