Introduction: Ventricular septal defect (VSD) is one of the most common congenital heart defects. We aimed to determine the prevalence of VSD in a population-based cohort of newborns and assess the rate of spontaneous closure during the first 12 months of life. Methods: The Copenhagen Baby Heart Study (CBHS) is a population-based cohort study, including more than 25,000 newborns born in the greater Copenhagen area. Newborns underwent echocardiography within 60 days of birth. Newborns with VSDs had echocardiographic follow-up after 3, 6, and 12 months. Results: A total of 850 newborns (3.3% of 25.556) with a VSD were identified in the CBHS. Of these, 787 (92.6% [95% CI 90.1-94.2]) were muscular VSDs, 60 (7.0% [95% CI, 5.5-9.0]) were perimembranous, and 3 (0.4% [95% CI, 0.0-1.1]) were subarterial. After 1 year, 83.5% (607 of 727) of all VSDs had closed spontaneously, resulting in a decrease of prevalence from 3.3% at birth to 0.5% in 1-year old children. Muscular VSDs showed significantly higher rate of spontaneous closure compared with perimembranous VSDs (86.9% (582/670) vs. 46.9% (25/54), p < 0.001). Determinants associated with spontaneous closure were smaller size of the VSD (p < 0.001) and the absence of multiple VSDs (p < 0.0025). Conclusion: The prevalence of VSDs in unselected newborns was 3.3%. Almost 9/10 of all VSDs identified in newborns, close spontaneously during the first year of life, ultimately resulting in a prevalence of VSD in 1-year-old children of 0.5%. The identified factors associated with spontaneous closure were muscular type, small size, and absence of multiple VSDs.