The objectives of this study were to determine the protein molecular structures of the new coproducts from bioethanol production, quantify protein structure amide I to II and alpha-helix to beta-sheet spectral peak intensity ratio, and illustrate multivariate molecular spectral analyses as a novel research tool for rapid characterization of protein molecular structures in bioethonal bioproducts. The study demonstrated that the grains had a significantly higher ratio of alpha-helix to beta-sheet in the protein structure than their coproducts produced from bioethanol processing (1.38 vs 1.03, P < 0.05). There were significant differences between wheat and corn (1.47 vs 1.29, P < 0.05) but no difference between wheat dried distiller grains with solubles (DDGS) and corn DDGS (1.04 vs 1.03, P > 0.05). The grains had a significantly higher ratio of protein amide I to II in the protein structure than their coproducts produced from bioethanol processing (4.58 vs 2.84, P < 0.05). There were no significant differences between wheat and corn (4.61 vs 4.56, P > 0.05), but there were significant differences between wheat DDGS and corn DDGS (3.08 vs 2.21, P < 0.05). This preliminary study indicated that bioethanol processing changes protein molecular structures, compared with original grains. Further study is needed with a large set of the new bioethanol coproducts to quantify protein molecular structures (alpha-helix to beta-sheet ratio; amide I to II ratio) of the bioethanol coproducts in relation to nutrient supply and availability in animals.