Recent global fluctuations in food prices and continuing environmental degradation highlight the future challenge of feeding a growing world population. However, current dialogues rarely address the relationship between agricultural changes and health. This relationship is traditionally associated with the role of food in nutrition and with food safety, and while these are key interactions, we show in this paper that the relationship is far more complex and interesting. Besides the direct effects of agriculture on population nutrition, agriculture also influences health through its impact on household incomes, economies and the environment. These effects are felt particularly in low- and middle-income countries, where dramatic changes are affecting the agriculture-health relationship, in particular the growth of nutrition-related chronic disease and the associated double burden of under- and over-nutrition. Greater understanding of the negative effects of agriculture on health is also needed. While lengthening food value chains make the chain of influence between agricultural policy, food consumption, nutrition and health more complex, there remain opportunities to improve health by changing agricultural systems. The first challenge in doing this, we suggest, is to improve our capacity to measure the impact of agricultural interventions on health outcomes, and vice versa.