In the sorghum-growing regions of the U.S., some bioethanol plants use mixtures of corn and sorghum grains as feedstocks depending on price and availability. For regulatory purposes and for optimizing the ethanol manufacturing process, knowledge of the grain composition of the milled feedstock is important. Thus, a near infrared spectroscopy method was developed to determine the content of sorghum in corn–sorghum flour mixtures. Commercial corn and sorghum grain samples were obtained from a bioethanol plant over an 18-month period and across two crop seasons. An array of corn–sorghum flour mixtures having 0–100% sorghum was prepared and scanned using a near infrared spectrometer in the 950–1650 nm wavelength range. A partial least squares regression model was developed to estimate sorghum content in flour mixtures. A calibration model with R2 of 0.99 and a root mean square error of cross validation of 3.91% predicted the sorghum content of an independent set of flour mixtures with r2 = 0.97, root mean square error of prediction = 5.25% and bias = −0.49%. Fourier-transform infrared spectroscopy was utilized to examine spectral differences in corn and sorghum flours. Differences in absorptions were observed at 2930, 2860, 1710, 1150, 1078, and 988 cm−1 suggesting that C–H antisymmetric and symmetric, C=O and C–O stretch vibrations of corn and sorghum flours differ. The regression coefficients of the near infrared model had major peaks around overtone and combination bands of C–H stretch and bending vibrations at 1165, 1220, and 1350 nm. Therefore, the above results confirmed that sorghum content in corn sorghum flour mixtures can be determined using near infrared spectroscopy.