In vivo electroporation is one of the most efficient methods for introducing the nucleic acids into the target tissues, and thus plays a pivotal role in gene therapeutic studies. In vivo electroporation in rodent brains is often involved in injection of nucleic acids into the brain ventricle or specific area and then applying appropriate electrical field to the correct area. Better understanding of the progress of electroporation in rodent brain may further facilitate gene therapeutic studies on some brain disorders. For this purpose, we briefly summarized the advantages, the procedures and recent progress of transferring nucleic acids into the rodent brain using in vivo electroporation.