Neurotrophin 3 (NT3) and its receptors are expressed throughout the gastrointestinal tract, especially in the enteric nervous system. However, little is known about the effects of NT3 on gastrointestinal motility. To investigate the effects of NT3 on gastric or colonic motility under baseline conditions, after subdiaphragmatic vagotomy and in a model of postoperative ileus. Sprague-Dawley rats were equipped with strain gauge transducers on the gastric or colonic wall. Motility was recorded for 30 min, followed by i.v. administration of NT3 and motility-recording for another 60 min. Experiments were performed on three consecutive days and separately in a postoperative ileus model. To evaluate a vagal pathway, experiments were also performed on vagotomized rats. NT3 inhibited gastric motility. This inhibitory effect was reduced by subdiaphragmatic vagotomy. Preoperative treatment with NT3 prolonged the postoperative gastric ileus compared to vehicle treatment. Colonic motility in the intact animal was unchanged by NT3, but was increased postoperatively. NT3 treatment inhibited gastric but not colonic motility. This inhibition of gastric motility seems to be partly mediated by the vagus nerve. NT3 aggravates gastric postoperative ileus but attenuates colonic postoperative ileus, which corresponds to the observed positive effects of NT3 on constipated patients.