Zinc-fingers are one of the known structural motifs present in DNA-binding regions of transcription factors. By using specific binding feature of zinc fingers to DNA triplets, a new generation of zinc finger endonucleases (ZFNs) have been designed for gene targeting. By this way, ZFNs cleavage double strand DNA on specific binding sites and stimulate repair processes. Homologous recombination, non-homologous end-joining or deletions/insertions can be occured at these sites during ZFN activity. By taking the advantage of design synthetic zinc finger nucleases, gene targeting (GT) was tested in various organisms (yeast, plant and mouse cell lines). This approach is promising for plant genetic engineering beacuse normally the integration of transgenes into plant genome occurs in a random manner which may result gene silencing or inactivity of other genes. Therefore, site-directed genomic applications will be useful to control integration patterns and proper transmission of transgenes to the generations in the future.