Transformation is the process by which the genetic make-up of an organism is altered by the insertion of new gene into its genome. As most of the agronomic traits are polygenic in nature, so the integration of multiple genes is required to manipulate the complex, polygenic metabolic or regulatory pathways, while ensuring their stable inheritance and expression in succeeding generations. There are various methods for multiple gene transformation but co-transformation method has proved more efficient and transplastomic technology can be used whenever have an option. It has many applications in plant breeding such as enhancing nutritional value like β-carotene content in rice, canola, maize and potato, vitamin E content in Arabidopsis, canola and soybean, synthesis of PUFA in Arabidopsis, impart biotic and abiotic stress resistance. Also, MGT has applications in molecular pharming.