Short-chain fatty acids (SCFA) are monocarboxylates produced by bacterial fermentation that play a crucial role in maintaining homeostasis in the large intestine. Two major transporters for SCFA, monocarboxylate transporter (MCT) and slc5a8 (or SMCT), exist in the digestive tract. The present histochemical study using in situ hybridization and immunohistochemistry revealed the distribution and subcellular localization of the MCT family in the digestive tract of mice, rats, and humans, comparing these with that of slc5a8. The expression of mucosal MCT1 in the mouse and rat was most intense in the cecum, followed by the colon, but low in the stomach and small intestine. Among other MCT subtypes, only MCT2 was detected in the parietal cell region of the gastric mucosa. Slc5a8 had predominant expression sites in the distal half of the large bowel and in the most terminal ileum. The mucosal MCT1 was localized in the basolateral membrane of enterocytes, while slc5a8 was restricted to the apical cell membrane, suggesting the involvement of slc5a8 in the uptake of luminal SCFA, and of MCT1 in the efflux of SCFA and monocarboxylate metabolites towards blood circulation. The large intestine expressed both types of the transporter, but their distribution patterns differed along the longitudinal axis of the intestine and along the perpendicular axis of the mucosa.