Background: Vitamin D levels are known to be associated with atopic disease development; however, existing data are controversial. The aim of this study was to investigate whether corresponding maternal and cord blood vitamin D levels are associated with atopic outcomes in early infancy. Methods: Within the LINA cohort study (Lifestyle and environmental factors and their Influence on Newborns Allergy risk), 25(OH)D was measured in blood samples of 378 mother�child pairs during pregnancy and at birth. Information about children's atopic manifestations during the first 2 years of life was obtained from questionnaires filled out by the parents during pregnancy and annually thereafter. Cord blood regulatory T cells (Treg) were detected by methylation-specific PCR using a Treg-specific demethylated region in the FOXP3 gene. Results: The median maternal 25(OH)D3 level was 22.19 ng/ml (IQR 14.40�31.19 ng/ml); the median cord blood 25(OH)D3 10.95 ng/ml (6.99�17.39 ng/ml). A high correlation was seen between maternal and cord blood 25(OH)D3 levels, both showing a seasonal distribution. Maternal and cord blood 25(OH)D3 was positively associated with children's risk for food allergy within the first 2 years. Further, higher maternal 25(OH)D3 resulted in a higher risk for sensitization against food allergens at the age of two. Cord blood 25(OH)D3 levels were negatively correlated with regulatory T cell numbers. Conclusion: Our study demonstrates that high vitamin D levels in pregnancy and at birth may contribute to a higher risk for food allergy and therefore argues against vitamin D supplement to protect against allergy.