<b><i>Introduction:</i></b> The serotonin 3A receptor (5-HT<sub>3A</sub>R) is involved in vomiting and gastrointestinal motility. However, it is not well understood the expression pattern of 5-HT<sub>3A</sub>R in the gut immunohistochemically and how much contribution of 5-HT<sub>3A</sub>R to upper or lower intestinal motility. <b><i>Objectives:</i></b> We investigated the contribution of 5-HT<sub>3A</sub>R to gastrointestinal motor function by using 5-HT<sub>3A</sub>R KO mice and sought to identify 5-HT<sub>3A</sub>R-expressing cells via immunohistochemical staining using 5-HT<sub>3A</sub>R-GFP reporter mice. <b><i>Methods:</i></b> The expression of 5-HT<sub>3A</sub>R was measured in each section of the gut through real-time PCR. The motor function of the stomach and colon was assessed via the <sup>13</sup>C-octanoic acid breath test and colonic bead expulsion test, respectively, using 5-HT<sub>3A</sub>R KO mice. 5-HT<sub>3A</sub>R-expressing cells in the muscle layer of the gut were identified by immunohistochemical staining using 5-HT<sub>3A</sub>R-GFP reporter mice. <b><i>Results:</i></b> 5-HT<sub>3A</sub>R was expressed throughout the digestive tract, and 5-HT<sub>3A</sub>R expression in the stomach and lower digestive tract was higher than that in the other sections. Motor function in the stomach and colon was lower in 5-HT<sub>3A</sub>R KO mice than in WT mice. As a result of immunohistochemical staining using GFP reporter mice, cholinergic neurons and PDGFRα<sup>+</sup> cells were shown to express 5-HT<sub>3A</sub>R. In contrast, 5-HT<sub>3A</sub>R indicated by GFP fluorescence was rarely detected in ICC and smooth muscle cells. <b><i>Conclusions:</i></b> These results show that 5-HT<sub>3A</sub>R is highly expressed in the stomach and large intestine and that the activation of 5-HT<sub>3A</sub>R accelerates gastric emptying and large intestine transit. Additionally, 5-HT<sub>3A</sub>R is highly expressed in cholinergic neurons and some interstitial cells, such as PDGFRα<sup>+</sup> cells.