Background: A complex interaction between environmental and lifestyle factors, immune dysregulation, and skin barrier integrity is believed to contribute to the development of atopic dermatitis (AD). However, the precise mechanisms underlying disease onset in infants remain largely unclear. Methods: The ‘Munich Atopic Prediction Study’ (MAPS) is a comprehensive clinical and laboratory investigation of a prospective birth cohort from Munich, Germany. Information on pregnancy, child development, environmental influences, parental exposure to potential allergens, as well as illnesses affecting both children and parents is gathered through questionnaires. This is complemented by thorough clinical examinations conducted by trained dermatologists, with a focus on allergies and skin health. Biomarker analyses were performed on cord blood immune cells using flow cytometry. Results: Our analysis revealed an altered immune profile in the cord blood of infants who later developed AD, characterized by reduced frequencies of CD4 + T cells and increased B cell counts. Remarkably, however, regulatory B (Breg) cell frequencies were significantly reduced in these infants. Furthermore, our findings suggested that maternal allergen-specific immunotherapy may have a beneficial effect on the development and frequency of Breg cells. Conclusion: Our study identifies early immune alterations, particularly a reduction in cord blood Breg cells, as potential contributors to AD pathogenesis. These findings demand further research on B cells in the development of atopic diseases as B cells may participate in the initiation or prevention of these diseases. Specifically, inclusion of Breg cell measurements in neonatal immune panels could support early risk stratification and perceptively even personalized prevention of atopic diseases.