Neuroendocrine cells (NEC) are a cell population in the gastrointestinal tract that plays a role in the regulation of the digestion process, satiety and nutrient homeostasis. NE cells express a variety of bioactive hormones that can undergo changes in response to different luminal stimuli, including multiple components, which are present in the diet. In recent years, a modern (hybrid) type of rye grain has been introduced to feed industry. The goal of the present study was to determine immunohistochemically whether the feeding of the pigs with population and hybrid rye grains may evoke adverse changes in the small and large intestines in terms of the expression of serotonin, glucagon-like peptide 1 (GLP1) and somatostatin. Feeding animals with population and hybrid rye grains resulted in a slight increase in serotonin-positive NE cells in the small intestine (but not in the large intestine). After feeding animals with population rye (but not with hybrid rye) grains, there was a decrease in the small intestine GLP1-immunoreactive NE cells was found. No changes in the expression of GLP1 were found in the large intestine of experimental animals. The numbers of somatostatin-IR NEC in the small and large intestines were not affected by feeding with either population or hybrid rye grains. In conclusion, we found that feeding pigs with hybrid and population rye grains started adaptive changes in NEC. However, those changes were not profound, which allows us to speculate that adverse effects of these rye grains have a minor (if any) impact on the gut hormone balance (and indirectly on the health status) of animals.