Newborns with congenital heart defects (CHD) have smaller heads at birth and CHD is associated with impaired neurodevelopment. How and when fetal brain growth is disrupted in CHD remains unknown. We aimed to estimate the association between fetal CHDs and head size at three time points during pregnancy; the end of the 1st trimester, during the 2nd trimester and at birth. We identified fetuses diagnosed with a CHD either during pregnancy or up to 12 months after birth in a population-based 2-year pregnancy cohort in Western Denmark. The brain growth parameters in fetuses with CHD were compared to those of the fetuses from the general population at three time points: 1st trimester biparietal diameter Z-score, 2nd trimester head circumference Z-score and head circumference Z-score at birth. Fetuses from multiple gestations, and fetuses with genetic syndromes or major extra cardiac malformations were excluded from the main analyses. We obtained data from 63.201 pregnancies. Three hundred fetuses were included in the main analyses; 149 with major and 151 with minor CHD. First trimester mean biparietal diameter Z-score in fetuses with CHD did not differ from that of fetuses in the general population. Second trimester mean head-circumference Z-score in fetuses with major CHD were statistically significantly below that of the general population; -0.2 (95% CI -0.4;-0.07, P