To investigate the ability of corn germ to withstand the fuel ethanol fermentation process without major damage to germ integrity and germ oil quality, five treatments were designed to explore degerming before fermentation (front-end) and after fermentation (tail-end), and the feasibility of breaking the kernel with minimum shear forces (wet-split). Germ from low-shear (wet-split) tail-end degerming maintained its integrity during the process. The wet-grind pretreatment caused 22% germ damage, and the subsequent fermentation caused 18% additional germ damage. The germ recovered after fermentation showed physical strength similar to that of those isolated by wet means before fermentation. The oils extracted from the tail-end germ fractions had the same low free fatty acid (FFA) content (2%) and similar low peroxide value (2 meq/kg) as those extracted at the front end. The good oil quality of the tail-end germ fraction was attributed to excellent germ integrity. The oil recovered after traditional dry-grind ethanol production was highly deteriorated, with 22% FFAs and 9 meq/kg peroxide value because the germ was broken into small pieces during dry grinding. So long as kernel-breakage or size-reduction pretreatments are conducted to retain intact germs or keep them in large pieces before fermentation, the germ can survive the cooking, starch hydrolysis, and yeast metabolism during the ethanol fermentation process. These findings lay a foundation for developing new degerming strategies where the germ can be isolated during or after fermentation, which could be easily integrated into the conventional dry-grind corn ethanol process.