Background: The gut is the body’s major immune structure, and the gut mucosa, which contains intraepithelial lymphocytes (IELs) and subepithelial natural immune cells, is considered the primary site for eliciting local immune responses to foreign antigens. Pigs are susceptible to intestinal infections at all life stages; however, neonates tend to be the most susceptible. This study compared the small intestine of neonatal and weaned piglets to provide a theoretical basis for preventing intestinal infectious diseases in neonatal piglets. Results: Histological analyses of weaned piglet intestines showed increased crypt depth, higher IEL count, and larger ileal Peyer’s patches compared with those of neonates. Additionally, the ileal villi of weaned piglets were longer than those of neonatal piglets. The expression of claudin-3 and occludin protein was remarkably higher in weaned piglets than in neonatal piglets. The numbers of CD3 + T cells, goblet cells, and secretory cells were also higher in the small intestine of weaned piglets than in those of neonates. The number of secretory IgA-positive cells in the jejunum was not significantly different between neonatal and weaned piglets. The gene expression of 12 pattern recognition receptors (PRRs), such as TLR1–10, MDA5, and RIG-I in the small intestines of both neonatal and weaned piglets was also examined. The mRNA expression of most pattern recognition receptors genes in the duodenum and jejunum was higher in weaners than in neonates; however, the inverse was true in the ileum. Compared with that in weaned piglets, there were significantly fewer CD3 + , CD4 + , and CD8 + T cells from peripheral blood-mononuclear cells in neonatal piglets. Conclusions: In this study, the physical and immunological components of small intestines of neonatal and weaned piglets were investigated. Our results provide preliminary data on differences in the immune mechanisms between the small intestines of 0- and 21-day-old piglets. Future studies could focus on additional developmental stages of pigs and how the differences in their small intestines affect the animal’s response to pathogens