Malformations of cortical development (MCDs) are heterogonous neurodevelopmental disorders that often result in epilepsy and developmental delay in children. To date, the genetic causes of a number of MCDs have been identified, including microcephaly (e.g., MCPH1, ASPM, CPAP, CDK5RAP2, and STIL), lissencephaly (e.g., LIS1, DCX, ARX, and TUBA1A), double cortex (e.g., DCX), periventricular nodular heterotopia (e.g., ARFGEF2), and tuberous sclerosis (e.g., TSC1 and TSC2). However, many genetic mutations involved in MCD pathogenesis still remain unidentified. Here we developed an in vivo genetic screen paradigm that utilizes in utero electroporation of transposons into mouse embryos to induce insertional mutations in neural stem cells (i.e., radial glial cells; RGCs). We identified 33 potential MCD genes, many of which have been previously implicated in neuronal development and related disorders, including holoprosencephaly, microcephaly and mental retardation. Bioinformatics analysis demonstrated that these candidate genes are highly associated with neuronal development and various neuronal disorders. To verify the clinical relevance of these candidate genes, we analyzed somatic mutations in brain tissue from patients with focal cortical dysplasia (FCD) using deep whole exome sequencing (WES) and found multiple mutations in many of these candidate genes. Functional knockdown of these genes in vivo by RNA interference (RNAi) or CRISP/Cas9 technology causes alterations in the distribution of neurons within the developing neocortex that are consistent with the screening results. These findings demonstrate that our new approach is able to mimic MCD pathogenesis and to identify various novel genes and pathways involved in cortical development.