In the past few years, the increasing accessibility of next-generation sequencing technology has translated to a number of significant advances in our understanding of brain malformations. Genes causing brain malformations, previously intractable due to their complex presentation, rarity, sporadic occurrence, or molecular mechanism, are being identified at an unprecedented rate and are revealing important insights into central nervous system development. Recent discoveries highlight new associations of biological processes with human disease including the PI3K-AKT-mTOR pathway in brain overgrowth syndromes, the trafficking of cellular proteins in microcephaly-capillary malformation syndrome, and the role of the exosome in the etiology of pontocerebellar hypoplasia. Several other gene discoveries expand our understanding of the role of mitosis in the primary microcephaly syndromes and post-translational modification of dystroglycan in lissencephaly. Insights into polymicrogyria and heterotopias show us that these 2 malformations are complex in their etiology, while recent work in holoprosencephaly and Dandy-Walker malformation suggest that, at least in some instances, the development of these malformations requires "multiple-hits" in the sonic hedgehog pathway. The discovery of additional genes for primary microcephaly, pontocerebellar hypoplasia, and spinocerebellar ataxia continue to impress upon us the significant degree of genetic heterogeneity associated with many brain malformations. It is becoming increasingly evident that next-generation sequencing is emerging as a tool to facilitate rapid and cost-effective molecular diagnoses that will be translated into routine clinical care for these rare conditions in the near future.