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Flour can undergo a variety of changes as it is subjected to the extreme pressure, shear, and heat within an extruder. The chemical changes that occur can lead to a vast difference in product quality, texture, and taste. While a majority of research has explored final product chemical qualities and starting material qualities, it is also important to understand the changes occurring within the extruder as the process variables change. In order to understand these changes, waxy wheat flour was extruded in a co-rotating twin screw extruder and brought to a dead stop under different extrusion conditions. By quickly opening the extruder, samples of starch were retrieved from the feed, transition, and cooking zones of the barrel. Through degree of gelatinization, viscometry, and HPLC results, it was shown that the starch components gelatinized and degraded quickly through the transition zone and slowly through the cooking zone. Additionally, temperature and screw configuration played a significant role in altering the amount of degradation and gelatinization. Results were also correlated to water solubility and expansion measurements so that the amount of starch degradation could be linked to end product quality. By understanding the chemical changes occurring within the extruder and linking them to the end product quality, the process can be manipulated more accurately to achieve desired food products.