Agricultural production, food systems and population health are intimately linked. While there is a strong evidence base to inform our knowledge of what constitutes a healthy human diet, we know little about actual food production or consumption in many populations and how developments in the food and agricultural system will affect dietary intake patterns and health. The paucity of information on food production and consumption is arguably most acute in low- and middle-income countries, where it is most urgently needed to monitor levels of under-nutrition, the health impacts of rapid dietary transition and the increasing 'double burden' of nutrition-related disease. Food availability statistics based on food commodity production data are currently widely used as a proxy measure of national-level food consumption, but using data from the UK and Mexico we highlight the potential pitfalls of this approach. Despite limited resources for data collection, better systems of measurement are possible. Important drivers to improve collection systems may include efforts to meet international development goals and partnership with the private sector. A clearer understanding of the links between the agriculture and food system and population health will ensure that health becomes a critical driver of agricultural change.