Plants provide the major part of human food intake. Whilst advances in agronomic characteristics (improved yield and better pest and disease resistance) continue to be a very high priority, there is increasing opportunity to enhance the nutritional value of plant based diets by improving the nutritional quality of staple foods. We now have proof of principle that genetic engineering can be used to produce plant-derived human vaccines. In relation to plant foods for human health, the research challenges include understanding: (1) why certain foods cause adverse reactions in some individuals but not in others; (2) the mechanisms of action of apparently ‘protective’ foods such as fruits and vegetables. There is also a need to develop much more informative and robust methods for measuring dietary exposure to specific plant foods or food constituents, including both recent exposure, for which a metabolomics approach may be particularly helpful, and long-term exposure.