The role of breastfeeding in the development of the cellular immune system, antimicrobial strategies of neutrophils, and local cytokine levels was evaluated in a single-center, prospective, open-label, uncontrolled study of healthy infants who were either naturally or artificially breastfed. The main group included practically healthy children who were exclusively breastfed for the first year of life. Thirty-six children were examined during the first stage and 25 from this group during the second stage. The comparison group included children who received an adapted cow’s milk formula during the first half-year of their lives and a different formula during the second half-year. Thirty-one children were examined during stage one and 27 from this group were examined during stage two. A comprehensive study of mucosal immunity was conducted, assessing the cytokine profile and cellular components using the method of smear prints from the nasal mucosa. The results showed that the nature of feeding during the first year of life influences the formation of mucosal immunity and programming the postnatal development of the child’s immunological reactivity. In the absence of the immunomodulatory effects of breast milk, there is an imbalance in the cytokine profile, with a physiological deviation of the immune response linked to the predominance of Th2 profiles. In contrast, breastfeeding promotes the optimal cellular composition of the upper respiratory mucosa and a cytomorphological neutrophil profile with minimal destructive changes. Breastfeeding programs the optimal functional profile of neutrophils, including the level of receptor activity, intracellular biocidal activity, cytotoxicity, ability to complete phagocytosis. This natural infant feeding method has a long-term protective effect, preventing neutrophil destruction under the influence of environmental factors and respiratory viral agents, and ensuring optimal mucosal immunity development in the respiratory tract.