Atrial septal defect (ASD) is characterized by a left-to-right shunt causing dilatation of the right atrium and right ventricle as well as pulmonary hyperperfusion. The detection of ASDs often occurs late in childhood or adulthood. Little is known about cardiac structure and function in neonates with ASD. We analyzed neonatal echocardiograms from the Copenhagen Baby Heart Study, a multicenter, population-based cohort study of 27,595 neonates. We included 716 neonates with secundum-type ASDs and matched them 1:1 on sex and age at examination with neonates without ASD from the same birth cohort. Neonates with an ASD (median age 11 days, 52% female) had larger right ventricular (RV) dimensions than matched controls (RV longitudinal dimension end-diastole: 27.7 mm vs. 26.7 mm, p < 0.001; RV basal dimension end-diastole: 14.9 mm vs. 13.8 mm, p < 0.001; and RV outflow tract diameter 13.6 mm vs. 12.4 mm, p < 0.001). Atrial volumes were larger in neonates with ASD compared to controls (right atrial end-systolic volume: 2.9 ml vs. 2.1 ml, p < 0.001; and left atrial end-systolic volume 2.0 ml vs. 1.8 ml, p < 0.001). Tricuspid annular plane systolic excursion was larger in neonates with ASD than in controls (10.2 mm vs. 9.6 mm, p < 0.001). Left ventricular dimensions and function did not differ between neonates with ASD and controls. In conclusion, ASDs were associated with altered cardiac dimensions already in the neonatal period, with larger right ventricular dimensions and larger atrial volumes at echocardiography within the first 30 days after birth. ClinicalTrials.gov Identifier: NCT02753348 (April 27, 2016).