By using a systems analytical model (SAM) and a fuzzy logic control software (fuzzy CIM) extrusion experiments were designed, that enabled a differentiation of the influence of the thermal energy input, expressed by the product temperature (PT), and the influence of the specific mechanical energy input (SME) on the molecular structure of extruded starch. The chromatographic examination of the molecular changes in the starch clearly revealed the influence of the extrusion cooking conditions on molecular degradation.The molecular size of extruded starch, expressed as the weight average of the molecular weight (M __ w ), decreased exponentially when SME increased. In the range of 110-180 °C, PT had no significant influence on M __ w so that the observed reduction of M __ w was primarily dependent on the increase in SME. By contrast, the polydispersity depended both on PT and SME. The influence of PT on the polydispersity was of minor significance up to 160 °C, increasing more steeply at higher temperatures. PT increase above 180 °C resulted in increasing reducing power of the extruded starch, whereas SME had almost no effect on reducing power. Only at a PT of more than 180 °C small amounts of short chain molecules with a degree of polymerisation (DP) smaller than 6 could be determined.