Resistant starch (RS) is defined as the fraction of starch that escapes digestion in the small intestine, serving as a fermentation substrate for beneficial colonic bacteria. Several studies have been focused on the description of the RS fractions from different starch varieties, but little attention has been paid to the digestion process itself that, from the present work, seems to play a key role in the generation of enzyme-RS (ERS), as determined in vitro. High-amylose starch samples, extruded at two different processing conditions, have been characterized at different stages of in vitro digestion using scanning electron microscopy (SEM), small-angle X-ray scattering (SAXS), infrared spectroscopy (FF-IR), solid state C-13 NMR spectroscopy, and X-ray diffraction (XRD). Control samples kept for 18 h in the digestion solution without starch hydrolyzing enzymes (alpha-amylase and amyloglucosidase) were used for comparison purposes. An increase in molecular order was favored by the hydrolytic action of the enzymes, reflected in an increase in double helical order observed by NMR, higher crystallinity measured by XRD, and corresponding changes in FT-IR spectra. An increase in the intensity of the scattering objects was also observed by SAXS as a function of digestion. SAXS from the dry ERS fractions reveals the 001 reflection of crystallites formed during the digestion process, corresponding to a characteristic dimension of the resistant crystalline fraction of similar to 5 nm. The changes found suggest that enzyme resistant starch does not refer to a specific structure present in predigested starches, but may in fact be formed during the digestion process through the rearrangement of amylose chains into enzyme-resistant structures of higher crystallinity. Therefore, the resistance to enzyme digestion of a specific processed starch is the result of a competition between the kinetics of enzyme hydrolysis and the kinetics of amylose retrogradation.