BackgroundCongenital heart disease (CHD) is common and is associated with impaired early brain development and neurodevelopmental outcomes, yet the exact mechanisms underlying these associations are unclear.PurposeTo utilize MRI data from a cohort of fetuses with CHD as well as typically developing fetuses to test the hypothesis that expected cerebral substrate delivery is associated with total and regional fetal brain volumes.Study TypeRetrospective case–control study.PopulationThree hundred eighty fetuses (188 male), comprising 45 healthy controls and 335 with isolated CHD, scanned between 29 and 37 weeks gestation. Fetuses with CHD were assigned into one of four groups based on expected cerebral substrate delivery.Field Strength/SequenceT2‐weighted single‐shot fast‐spin‐echo sequences and a balanced steady‐state free precession gradient echo sequence were obtained on a 1.5 T scanner.AssessmentImages were motion‐corrected and reconstructed using an automated slice‐to‐volume registration reconstruction technique, before undergoing segmentation using an automated pipeline and convolutional neural network that had undergone semi‐supervised training. Differences in total, regional brain (cortical gray matter, white matter, deep gray matter, cerebellum, and brainstem) and brain:body volumes were compared between groups.Statistical TestsANOVA was used to test for differences in brain volumes between groups, after accounting for sex and gestational age at scan. P_FDR‐values <0.05 were considered statistically significant.ResultsTotal and regional brain volumes were smaller in fetuses where cerebral substrate delivery is reduced. No significant differences were observed in total or regional brain volumes between control fetuses and fetuses with CHD but normal cerebral substrate delivery (all P_FDR > 0.12). Severely reduced cerebral substrate delivery is associated with lower brain:body volume ratios.Data ConclusionTotal and regional brain volumes are smaller in fetuses with CHD where there is a reduction in cerebral substrate delivery, but not in those where cerebral substrate delivery is expected to be normal.Evidence Level3Technical EfficacyStage 3