The food system is undergoing significant structural change at local, national, and international levels. As the food system evolves, some segments along the chain between producers and consumers are disappearing. Others are being transformed. Supply chain concepts are useful for identifying and assessing alternative designs for the reconfiguration of food product production systems. Changes in the food system will require farm managers to adopt new ways of thinking and new perspectives on collaboration with trading partners. They also will require farm management economists to draw on a wider set of economic theories and concepts than we have in the past. This paper begins with brief descriptions of emerging supply chains for high quality food products in the U.S.: (i) a branded product chain, (ii) a genetics-based chain, and (iii) a production-practice based chain. These illustrate the variety of emerging supply chain structures and the challenges firms face in designing new supply chains. The next section presents an overview of key elements of four theoretical frameworks that are helpful in supply chain analysis and design : (i) transaction cost economics, (ii) agency theory, (iii) property rights theory, and (iv) the resource based view of the firm. Concepts from these theories are used to explain structural differences in the three illustrative cases. Looking to the future, key challenges include improving system-wide efficiency through information sharing and logistics management, promoting transparency and trust among trading partners, and designing incentive systems that ensure an equitable distribution of costs and returns.