Background and aims Neurodevelopmental disorders are common in children with congenital heart disease (CHD) and largely ascribed to prenatal factors such as impaired cerebral growth. It remains to be established whether this is due to impaired intrauterine cerebral blood flow or genuine genetic causes. Down syndrome (DS) is a known cause of CHD, neurodevelopmental disorders and microcephaly. Hence, studies on DS may provide insight into the causes of impaired cerebral growth in CHD. We aimed to assess the risk of microcephaly in children with DS and CHD compared to children with DS and no CHD. Methods Children with DS (n = 389) and specific birth characteristics were identified in national registries. Head circumference and the risk of microcephaly (head circumference <-2SD) was compared between children with CHD (n = 168) and children without CHD (n = 221) by linear and logistic regression analyses (unadjusted and adjusted for gender and gestational age). Results There was no difference in head circumference between the groups, 0.0 cm (95% CI -0.4-0.4). Adjustment did not significantly alter the results. The risk of microcephaly was slightly higher in newborns with CHD, OR 1.4 (95% CI 0.8-2.6). Adjustment did not significantly alter the results. Conclusions We did not find indications of impaired head growth in children with DS and concomitant CHD. There might be a slight increase in the risk of microcephaly. We suggest that the most common types of CHD in DS i.e. atrioventricular septal defects, ventricular septal defects and atrial septal defects do not impair prenatal cerebral growth in children with DS.