Apelin is considered an important gut regulatory peptide with potential physiological roles in gastrointestinal cytoprotection and regulation of food intake and drinking behavior. The aim of this study was to determine the effects of intraperitoneal or intragastric apelin administration on gastric and intestinal epithelial apoptosis, mitosis and DNA repair enzyme 8-oxoguanine (OGG 1/2) expression in young Wistar rats (50 ± 5 g b. wt.). Apelin-13 was intraperitoneally or intragastrically administered twice a day for 10 days (100 nmol/kg b. wt./2 × day), and control groups received physiological saline as a placebo. The rats were sacrificed after treatment, and the gastric fundus, duodenum, middle jejunum and colon tissue samples were harvested for immunofluorescence studies. Intragastric administration of apelin-13 increased the apoptotic index in the stomach and colon tissues (P ≤ 0.001) but decreased apoptosis in the duodenum and jejunum (P < 0.001); this approach reduced the number of mitotic cells in the jejunum and colon but increased mitoses (P < 0.001) in the duodenum. Finally, intragastric apelin-13 increased (P < 0.001) OGG 1/2 enzyme expression in the stomach and jejunum and decreased its expression in the colon (P < 0.01). However, intraperitoneal apelin-13 injection caused the opposite effect in the same regions of the gastrointestinal tract. In conclusion, apelin inhibits gastrointestinal tissue maturation in young rats, regardless of the administration route. However, further studies are required to clarify the mechanism of apelin action on gastrointestinal tract maturation in young rats.