The CRISPR/Cas9 system has recently been adapted for generating knockout mice to investigate physiological functions and pathological mechanisms. Here, we report a highly efficient procedure for brain-specific disruption of genes of interest in vivo. We constructed pX330 plasmids expressing humanized Cas9 and single-guide RNAs (sgRNAs) against the Satb2 gene, which encodes an AT-rich DNA-binding transcription factor and is responsible for callosal axon projections in the developing mouse brain. We first confirmed that these constructs efficiently induced double-strand breaks (DSBs) in target sites of exogenous plasmids both in vitro and in vivo. We then found that the introduction of pX330-Satb2 into the developing mouse brain using in utero electroporation led to a dramatic reduction of Satb2 expression in the transfected cerebral cortex, suggesting DSBs had occurred in the Satb2 gene with high efficiency. Furthermore, we found that Cas9-mediated targeting of the Satb2 gene induced abnormalities in axonal projection patterns, which is consistent with the phenotypes previously observed in Satb2 mutant mice. Introduction of pX330-NeuN using our procedure also resulted in the efficient disruption of the NeuN gene. Thus, our procedure combining the CRISPR/Cas9 system and in utero electroporation is an effective and rapid approach to achieve brain-specific gene knockout in vivo.Technologies for disrupting the genome in living animals are essential for elucidating the physiological mechanisms of our body and the pathological mechanisms of diseases, and for contributing to the discovery of new therapeutic interventions for human diseases. One technique which has been widely utilized is homologous recombination-based gene targeting in embryonic stem (ES) cells 1 . In addition, conditional mutagenesis using ES cells that relies on the DNA recombinase Cre and its recognition site loxP has become a valuable tool to achieve gene targeting in selected cell types 2 . Although this gene targeting technology using ES cells is extensively utilized for generating various kinds of genetically modified mice, it is relatively arduous, costly and time-consuming.Recently, a simple and efficient genome targeting technology has been developed based on the microbial type II clustered, regularly interspaced, short palindromic repeats (CRISPR)/associated protein (Cas) adaptive immune systems derived from Streptococcus pyogenes 3 . Cas9 endonuclease guided by a duplex of mature CRISPR RNA (crRNA) and transactivating crRNA (tracrRNA) cleaves trespassing DNA from bacteriophages or plasmids in a sequence-specific manner 3 . In mammalian cells, it has been demonstrated that a combination of Cas9 and sgRNA, which is an artificial chimera of crRNA and tracrRNA, caused site-specific DSBs, and as a result, genome targeting via insertions and deletions (indels) was caused by error-prone non-homologous end-joining (NHEJ) 4,5 . These features of the CRISPR/Cas9 system facilitated the generation of mice carrying mutations in specific genes 6 . Indeed,...