Background Prospective studies of antenatal and infant vitamin D exposure and atopic disease from extensively characterised, disease-specific, maternal-infant cohorts with gold standard analysis of vitamin D status and clinically validated atopic outcomes are lacking. This study aimed to investigate associations between intrauterine vitamin D status and atopic outcomes in an extensively characterised, disease-specific, maternal-infant cohort. Methods Circulating 25-hydroxyvitamin D (25(OH)D) was measured in maternal sera at 15 weeks of gestation (n = 1537) and umbilical cord blood (n = 1050) using a CDC-accredited LC-MS/MS platform, and the association with clinically validated atopic disease outcomes (eczema, food allergy, asthma, allergic rhinitis) at 2 and 5 years was explored using multivariable logistic regression. Results Persistent eczema in the first 2 years of life was present in 5% of infants. Food allergy at 2 years was confirmed in 4%. The prevalence of aeroallergen sensitisation at 2 years was 8%. Asthma at 5 years was reported in 15% and allergic rhinitis in 5% of 5-year-olds. There were no significant differences in the distributions of maternal 25(OH)D at 15 weeks of gestation (mean [SD] 58.4 [26.2] and 58.5 [26.1] nmol/L) and cord 25(OH)D concentrations (mean [SD] 35.2 [17.8] and 35.4 [18.3] nmol/L) between children with and without atopic disease. Neither maternal (aOR [95% CI]: 1.02 [0.97, 1.08], P = 0.450) nor cord 25(OH)D (aOR [95% CI]: 1.00 [0.91, 1.09], P = 0.991) were significant predictors of atopic disease outcomes in fully adjusted models. Conclusion These data in a disease-specific cohort with prospectively collected, validated atopic outcomes do not support an association between antenatal exposure to vitamin D and atopic disease outcomes in childhood.