Abstract Targeted insertion and the precise deletion of DNA from transgenic plant chromosomes increase the potential of plant biotechnology for commercial applications and basic research. The Cre– lox recombination system is one of the best characterized and most widely used systems for these purposes. Cre– lox has many applications, but it is primarily used for the controlled excision of DNA fragments, in particular selectable marker genes, from the nuclear and chloroplast genomes, and for the targeted insertion of DNA into specific sites in the nuclear genome. Recent developments, including regulated expression of cre and the creative use of wild-type and modified lox sites, have improved the potential of these applications. After almost 15 years of research and development in plants, the Cre– lox system continues to provide an efficient and precise tool for plant biotechnologists.