Sufficient levels of vitamin D have been associated with higher chances for both clinical pregnancy and live birth among women undergoing assisted reproductive techniques, whereas low levels of maternal vitamin D have been associated with preeclampsia and late miscarriage. In Denmark, subgroups at risk for low vitamin D levels, including neonates and toddlers, are recommended to use supplementation. The aim was to study the level of vitamin D3 among neonates born after invitro fertilization compared with neonates from the general population. In this cohort study a random sample of 1326 neonates representing the general population and 1200 neonates conceived by invitro fertilization born in Denmark from 1995 to 2002 were identified from registries covering the whole Danish population. Information on use of assisted reproduction was collected from the Danish InVitro Fertilization register, ICD-10 code: DZ358F. 25-Hydroxyvitamin D was measured from dried blood spots routinely collected by heel prick 48-72 h after birth and corrected according to the hematocrit fraction for capillary blood of neonates. Linear regression analysis was performed, both crude and adjusted, for predefined putative confounders, identified through directed acyclic graphs. Vitamin D3 analysis could be performed from a total of 1105 neonates from the general population and 1072 neonates conceived by invitro fertilization that were subsequently included in the study. The median vitamin D3 was 24.0 nmol/L (interquartile range [IQR] 14.1-39.3) and 33.0 nmol/L (IQR 21.3-48.8) among neonates from the general population and neonates conceived by invitro fertilization, respectively. The adjusted mean difference between neonates from the general population and those conceived by invitro fertilization was 6.1 nmol/L (95% confidence interval 4.1-8.1). In this study, children born after invitro fertilization have a higher vitamin D3 than a random sample of neonates in Denmark.