Background Brain magnetic resonance imaging (MRI) of infants with congenital heart disease (CHD) shows brain immaturity assessed via a cortical-based semi-quantitative score. Our primary aim was to develop an infant paralimbic-related subcortical-based semi-quantitative dysmaturation score, a brain dysplasia score (BDS), to detect abnormalities in CHD infants and predict clinical outcomes. Our secondary aim was to validate our BDS in a preclinical mouse model of hypoplastic left heart syndrome. Methods A paralimbic-related subcortical BDS, derived from structural MRIs of infants with CHD, was correlated with clinical risk factors, regional cerebral volumes, feeding and 18-month neurodevelopmental outcomes. The BDS was validated in a known CHD mouse model named Ohia with two disease-causing genes, Sap130 and Pchda9. To relate clinical findings, RNA-Seq was completed on Ohia animals. Findings BDS showed high incidence of paralimbic-related subcortical abnormalities (including olfactory, cerebellar, and hippocampal abnormalities) in CHD infants (n=215) compared to healthy controls (n=92). BDS correlated with reduced cortical maturation, developmental delay, poor language and feeding outcomes, and increased length of stay. Ohia animals (n=63) showed similar BDS findings, and RNA-Seq analysis showed altered neurodevelopmental and feeding pathways. Sap130 mutants correlated with a more severe BDS whereas Pcdha9 correlated with a milder phenotype. Interpretation Our BDS is sensitive to dysmaturational differences between CHD and healthy controls, and predictive of poor outcomes. A similar spectrum of paralimbic-related subcortical abnormalities exists between human and Ohia mutants suggesting a common genetic mechanistic etiology.