California's fruit and nut tree crops represent one-third of the state's cash farm receipts and 70% of U.S. fruit and nut production. Advances in crop biotechnology and genetic engineering could help protect these valuable crops from pests and diseases and improve productivity. However, due to the difficulty of genetically engineering woody tree crops, as well as intellectual property concerns, regulatory hurdles and public perceptions about genetic engineering, biotechnology has not gained a foothold in this area of agriculture. Our survey of published genetic engineering research and issued field trial permits between 2000 and 2011 revealed that citrus and grape are the focus of most current work, and that walnut -not the more widely planted almond -is the focus among nut crops. Matching publicly funded genetic engineering research projects to a survey of the industry's top needs, we found that far less than half of the funded research has focused on the top-identified pest and disease threats. The most promising genetic engineering technology for fruit and nut tree crops may be transgrafting, which could address consumer concerns and benefit growers.