The key factor in production of fuel ethanol by simultaneous saccharification and fermentation is the efficient conversion of granular starch into ethanol. Most difficult stage in the process is the enzymatic hydrolysis of starch granules. Their supramolecular structure as well as crystallinity and presence of complexing agents are key factors for the hydrolysis process. The aim of the study was to examine structural changes in starch granules during the simultaneous processes of saccharification and fermentation of corn flour in the long-term repeated Simultaneous Saccharification and Fermentation (SSF) process with complete recycling of the stillage liquid fraction. The SSF experiments were performed using corn flour as a raw material, the STARGEN 001 preparation as a hydrolytic enzyme, and Red Star Ethanol Red (Saccharomyces cerevisiae ) fermentation yeasts. Residual starch structure after the 4 th , and the 7 th operation cycle was examined using scanning electron microscopy, X-ray diffractometry, IR spectroscopy as well as gel permeation chromatography. In spite of accumulating glycerol, organic acids and inorganic ions in the fermentation broth, the repeated batch SSF process, with stillage recycling into the fermentation phase conducted on corn flour with the use of the STARGEN 001 enzyme preparation, was found to run efficiently. The amount of unhydrolyzed residual starch was independent of the number of operation cycles. Hydrolysis of starch resulted in the formation of porous granules and a small amount of undigested granules and pyramid-shaped residuals. Crystalline and amorphous regions were evenly digested. The molecular mass distribution of residual starch after the SSF process significantly differed from that of native starch both in the region corresponding to amylopectin and to amylose, while the most distinctive changes with respect to the amylopectin/amylose ratio, i.e. in the 4th cycle the amylopectin content decreased by up to 19%.