Objective To investigate the distribution of the motilin receptor in the amygdala of rats and its role in regulating the duodenal migrating myoelectric complex (MMC). Methods The distribution of motilin receptor in the amygdala in adult SD rats was detected by immunohistochemistry methods, and the duodenal interdigestive MMC was recorded via the electrodes implanted in the duodenum and analyzed using a multichannel recorder. Results Motilin receptor was observed in the amygdala of rats. The great amount of motilin receptor was found in the medial amygdaloid nucleus, which was also abundant in the basolateral nucleus but less abundant in the basomedial amygdaloid nucleus, the central amygdaloid nucleus and the lateral amygdaloid nucleus. The shortening of the duodenal MMC cycle duration and the increase of the amplitude and the frequency of phase III were recorded after motilin receptors being bound with exogenous motilin in the amygdala. The effects could be completely blocked by the subdiaphragmatic vagotomy but not by the intravenous injections of atropine, phentolamine or propranolol. Anti-motilin serum could partially block these effects, and the destruction of the basolateral nucleus of the amygdala had no significant effects on the duodenal MMC. Conclusion Motilin receptor is present in all the subnuclei of the amygdala, with the greatest amount of motilin receptor present in the medial amygdaloid nucleus. Microinjections of motilin in the amygdala can shorten the duodenal MMC cycle duration and increase the amplitude and the frequency of phase III. These effects might be accomplished via the amygdala-hypothalamus-brainstem-vagus pathway, indicating the important role of the amygdala motilin receptor in the duodenal MMC regulation.