Fruits are one of the major sources of vitamins, essential nutrients, antioxidants and fibers in human diet. During the last two-three decades, genetic engineering methods based on the use of transgenes have been successfully adopted to improve fruit plants and focused mainly on enhanced tolerance to biotic and abiotic stresses, increased fruit yield, improved post harvest shelf life of fruit, reduced generation time and production of fruit with higher nutritional value. However, the development of transgenic fruit plants and their commercialization are hindered by many regulatory and social hurdles. Nowadays, new genetic engineering approaches i.e. cisgenesis or intragenesis receive increasing interest for genetic modification of plants. The absence of selectable marker gene in the final product and the introduced gene(s) derived from the same plant or plants sexually compatible with the target crop should increase consumer's acceptance. In this article, we attempt to summarize the recent progress achieved on the genetic engineering in fruit plants and their applications in crop improvement. Challenges and opportunities for the deployment of genetic engineering in crop improvement programs of fruit plants are also discussed. {\textcopyright} 2013 Springer Science+Business Media Dordrecht.