Genome editing with engineered nucleases is an emerging technology that enables manipulation of targeted genes in many organisms and cell lines. To date, two types of engineered nucleases have been developed. Zinc finger nucleases (ZFNs), which first emerged in 1996, have a long and successful history of genome editing. Transcription activator-like effector nucleases (TALENs), on the other hand, have been recently developed as a more user-friendly engineered nuclease, because TALENs are easy to construct in-house and the target site may be selected in any gene. Using these engineered nucleases, targeted gene disruptions have been achieved successfully in cultured cells and various organisms. Furthermore, gene correction or targeted gene addition have been reported mainly in cultured cells, and also in several organisms. Surprisingly, a third genome editing technology, known as CRISPR/Cas system, suddenly emerged in 2013 and efficient genome editing using this system was reported in various organisms. In this way, genome editing technology is now becoming the most exciting field in life sciences and important for developmental biology. We thought that it is a good timing to publish a special issue focusing on targeted genome editing. We hope this issue will provide general information on available techniques and materials for developmental biologists.