During the prenatal, neonatal, and weaning periods, the porcine gastrointestinal tract undergoes several morpho-functional, changes together with substantial modification of the microbial ecosystem. Modifications of the overall structure of the small intestine also occur, as well as a rapid increase of the volume, mainly in the last period of gestation: intestinal villi, starting from jejunum, appears shortly before the sixth week of gestation, and towards the end of the third month, epithelial cells diversify into enterocytes, goblet cells, endocrine, and Paneth cells. Moreover, in the neonatal period, colostrum induces an increase in intestinal weight, absorptive area, and brush border enzyme activities: intestine doubles its weight and increases the length by 30% within three days of birth. During weaning, intestinal environment modifies drastically due to a replacement of highly digestible sow milk by solid feed: profound changes in histological parameters and enzymatic activity are associated with the weaning period, such as the atrophy of the villi and consequent restorative hypertrophy of the crypts. All these modifications are the result of a delicate and precise balance between the proliferation and the death of the cells that form the intestinal mucosa (i.e., mitosis and apoptosis) and the health conditions of the piglet. An in-depth knowledge of these phenomena and of how they can interfere with the correct intestinal function can represent a valid support to predict strategies to improve gut health in the long-term and to prevent weaning gut alterations; thus, reducing antimicrobial use.