Gene site-specific insertion is an important tool to precisely integrate DNA molecules at a defined genomic location. Gene Targeting has many important implications in plant biotechnology such as creation of novel plant traits or the study of gene function. It requires the insertion of an extrachromosomal DNA into the plant cell that will be further integrated at a defined genomic locus through the use of the plant endogenous recombination machinery. Extensive efforts have been made to understand the mechanisms governing gene targeting and for establishing efficient system to achieve precise and efficient targeting. In particular the recent development of engineered nucleases represents an important step forward towards allowing the insertion of a transgene at any given locus in the genome.