In the weaning period, transition from sow's milk to the post-weaning diet causes the withdrawal of important nutrients as milk nucleotides, which are known to be determinant for the development of the gastrointestinal tract and immune function. The role of dietary nucleotides in the rebuilding of gut epithelium remains unclear. The aim of the study was to evaluate using appropriate markers the rate of mitosis (Ki67) in the crypt epithelial cell, and the rate of apoptosis (active caspase 3), autophagy (MAP I LC3) and DNA damage (p53) in the crypt and villi epithelial cells of the small intestine of weaned pigs fed diets supplemented without/with nucleotides. An in-tissue cytometry method, based on confocal imaging and automated quantitative analysis was implemented. The studies allowed us to understand molecular bases of animal performance which could not be accessed by a routine histometric approach. Namely, the dietary nucleotides provided more uniform small intestine epithelium with considerably less animal-to-animal variation in respect to mitosis (SEM = 1.02 in control vs. 0.62 in supplemented group), autophagy (SEM = 1.22 vs. 0.99) and expression of p53 protein (SEM = 0.72 vs. 0.28). A significant increase in ratio of apoptosis and autophagy, and significantly lower p53 expression was found in the nucleotide-supplemented pigs as compared to control. The mitosis/apoptosis index was lower in the nucleotide-supplemented group suggesting slower rebuilding of gut epithelium in these pigs as compared to the control, respectively 0.454 to 0.191. Finally, in the supplemented group a drop in p53 expression was observed, however, it remains uncertain whether the reduction in DNA damage index is due to the supplementation with nucleotides utilized as a source for repair processes or due to the reduced DNA alterations.