Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease associated with microcephaly and poor neurodevelopmental outcomes. Here we show that the Ohia HLHS mouse model, with mutations in Sap130, a chromatin modifier, and Pcdha9, a cell adhesion protein, also exhibits microcephaly associated with mitotic block and increased apoptosis leading to impaired cortical neurogenesis. Transcriptome profiling, DNA methylation, and Sap130 ChIPseq analyses all demonstrated dysregulation of genes associated with neurogenesis, cognitive impairment and autism. This involved perturbation of REST transcriptional regulation of neurogenesis, disruption of CREB signaling regulating synaptic plasticity, and defects in neurovascular coupling mediating cerebral blood flow. Adult mice harboring either the Pcdha9 mutation, which showed normal brain anatomy, or forebrain-specific Sap130 deletion via Emx1-Cre, which showed microcephaly, both demonstrated learning and memory deficits and autism-like behavior. These novel findings provide mechanistic insights indicating the adverse neurodevelopment in HLHS may involve cell autonomous/nonautonomous defects and epigenetic dysregulation. Overall design: Expression profiling using RNA-seq of 6 samples collected from forebrain of Sap130 conditional KO mice (n=3 at E14.5) and their littermate controls (n=3at E14.5).