The genome sequence of Arabidopsis is complete and the genomes of plants representing legumes (Medicago truncatula) and grasses (rice) will soon follow. The rate at which new genes have been discovered has far outstripped the pace at which their function is determined. The greatest hurdle that plant biologists face in assigning gene function and in crop improvement is the lack of efficient and robust technologies to generate gene replacements or targeted gene knockouts. Many of the factors underlying these events remain to be elucidated. This review addresses the current status of plant gene targeting and what is known about the associated plant DNA repair mechanisms.