Cooking extruders process a variety of foods, feeds, and industrial materials. Greater flexibility in product development with extruders depends upon understanding chemical reactions that occur within the extruder barrel and at the die. Starch gelatinization and protein denautration are the most important reactions during extrusion. Proteins, starches, and non-starch polysaccharides can fragment, creating reactive molecules that may form new linkages not found in nature. Vitamin stability varies with vitamin structure, extrusion conditions, and food matrix composition. Little is known about the effects of extrusion parameters on phytochemical bioavailability and stability. Reactive extrusion to create new flavor, antioxidant and color compounds will be an area of interest in the future.