Background: Functional gastrointestinal disorders are very common condition. The aim of this study is to evaluate the implications of the mode of pregnancy termination and early infant feeding on the incidence of gastrointestinal disorders and atopic dermatitis at birth and 3, 6, and 12 months of age. Methods: This study included 82 pregnant women and their newborns born at term. All newborns were examined at birth and 3, 6, and 12 months of age according to the ROME IV criteria. Results: In children born after cesarean section, the incidence of regurgitation was significantly higher. In children fed mostly or exclusively with formula, dry skin with allergic features was observed more often compared to breastfed children, but this relation was statistically significant only at the age of 12 months. The use of antibiotic therapy increased the risk of allergic skin lesions by almost seven times at 3 months of life. Gastrointestinal disorders in the form of regurgitation, colic, and constipation occur within the period of up to 12 months of the child's life and may be related to the mode of the termination of pregnancy via cesarean section and the use of artificial feeding or antibiotic therapy. The occurrence of atopic dermatitis in infants at 12 months of life is correlated with the mode of the termination of pregnancy after cesarean section. Conclusions: One of the risk factors for the occurrence of atopic dermatitis and gastrointestinal disorders in the period up to 12 months of the child's life may be a cesarean section and the use of formula feeding or antibiotic therapy.