The relationship between the interstitial cells of Cajal (ICC) and enteric nerves or smooth muscles cells is not fully defined. Presently, distribution and appearance of ICC in the rat stomach and duodenum was studied by immunohistochemistry, electron microscopy, and three-dimensional reconstruction. c-kit expressing ICC were regularly observed in the Auerbach's myenteric plexus (AP) of the stomach and duodenum. ICC in stomach and duodenum muscle layers was dissimilarly distributed. c-kit immunoreactive cells were sparsely distributed in the stomach circular muscle layer but were abundant in the duodenum deep muscular plexus (DMP). Electron microscopy revealed that stomach ICC-AP were irregular ovals with few cytoplasmic processes, and possessed an electron-dense cytoplasm, numerous mitochondria, intermediate filaments, and caveolae. Duodenum and stomach ICC-AP were similar in appearance. Ultrastructure observations and three-dimensional reconstructions revealed ICC-AP processes wrapping the nerve fibers and projecting into the space between smooth muscle cells. While ICC-AP was occasionally close to enteric nerves or smooth muscle cells, no connections were observed. ICC-DMP in duodenum was elongated and adopted the same cell axis orientation as the circular muscle cells. Unlike ICC-AP, ICC-DMP formed gap junctions with smooth muscle cells and had close contact with nerves. These results indicate that ICC-AP is regularly distributed in stomach and duodenum, while ICC-DMP is exclusively located in the duodenum. ICC-DMP, which possess gap junctions and closely contacts nerves, may participate in neuromuscular transmission.