The unravelling of the human genome has the potential to radically extend many of the strategies used in public health nutrition to improve health and to increase food availability, accessibility and utilization. The present paper divides nutrigenomics into two broad but differing areas in asking about possible public health applications: (1) the increasing mismatch between population growth and global food security, on top of the already approximately 800 million of the world population who are food insecure; (2) possible responses to the rising prevalence of non-communicable diseases as the Western diet becomes increasingly inappropriate to the needs of those consuming it. It is clear that complex interactions of multiple polymorphisms play a role in how individuals and sub-populations respond to dietary interventions. All these applications present public health and ethical challenges, particularly in ensuring that any benefits that do come from nutrigenomics are not restricted to the wealthy minority of only the affluent nations. The present paper concludes that the public health applications of nutrigenomics are probably at least a decade away, especially for developing countries. Clinical applications are likely to be more immediate, probably resulting in ‘designer diets’ for individuals with particular polymorphisms, but unless governments take on the role of ensuring some extent of equity in access, any benefits are most likely to go to those who can afford the screening, tests and treatment. At the same time, greatly increased international efforts are needed towards the continuing, and in some cases worsening, global malnutrition, as genetic manipulation of crops is unlikely to provide more than part of the solution.