Gelose 80, a high amylose maize starch, was extruded in a twin screw extruder at different feed moistures, cooled, stored for 12 days at 4°C, and cryo-milled. The raw and extruded starches were analysed for in vitro enzyme-resistant starch content (ERS), morphology, in vitro digestibility, long range (X-ray diffraction) and short range (FTIR) molecular order. Extrusion markedly increased the rate of starch digestion and reduced the ERS content, irrespective of whether B-type or B- and V-type polymorphs were present. Increasing feed moisture and storage resulted in only slight increases in ERS content, with X-ray diffraction and FTIR also showing small changes in long and short range molecular order, respectively. Analysis of residues from in vitro digestion showed the mechanism of enzyme resistance of granular and extruded high amylose starch to be markedly different, both qualitatively and quantitatively. Enzyme digestion of granular high amylose maize starch showed initial disorganization in structure followed by slow reorganization at later stages of digestion. In contrast, molecular reorganization took place throughout the enzyme digestion of extruded high amylose maize starch. Higher levels of crystallinity were found in digested extrudates compared with digested granules, showing that there is no direct correlation between starch crystallinity and enzyme digestion rates. © 2009, Elsevier Ltd.