Recent advances in plant molecular biology, functional genomics, and biochemistry have opened up a number of new avenues of research that will enable plant biologists to characterize, increase and modify plant content of a wide range of essential minerals and vitamins, as well as a number of secondary plant compounds that appear to play a role in improving human health and nutrition. In this review, several examples of exciting new research applying plant genomic and molecular genetic approaches to the improvement of phytonutrient content and composition in plants are presented. Research focusing on the elucidation of many of these complex biosynthetic and transport pathways in plants will require considerable resources in terms of funding, time, and personnel. As plant biologists move into interdisciplinary collaborations with nutritionists and food scientists, attention must be paid to a more complete identification and characterization of specific bioactive phytonutrients. Also, a more detailed assessment of the health-promoting properties of these compounds is needed, particularly for many of the secondary plant compounds for which clear epidemiologic and clinical data are still lacking. Finally, in order for significant progress to be made in modifying the nutrient composition of crops, a major investment must be made by funding agencies.