This introductory article to the special issue on ‘Food, agriculture and risk in contemporary Japan’ attempts to set the background to the theme by addressing trends and changes in the global agri-food system. These changes affect issues hinging on food, agriculture and risk in Japan. Against this backdrop, we argue that ‘risk’ is becoming an ever more important analytical category for understanding changes in Japan’s agri-food system given numerous phenomena that are perceived risky or unsafe. Although the contributions in this issue inevitably deal with various types of risks, among them two types of risks stand out in the analysis of the papers: economic risks that concern farmers’ livelihoods and health risk concerns stemming from food safety problems. The contributions shed light on how different actors deal with these risks and point to an interesting twist with regard to the question of agency; they show that consumers and farmers are not all that powerless.