This work aims at discriminating flours of 26 maize landraces from southern Brazil, by using the Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy and chemometrics (principal components analysis – PCA). PCA applied to the FTIR spectra in the 3-600 (whole spectrum) and 1650–1500 cm−1 (fingerprint region of proteins) spectral windows clearly discriminated the Amarelão landrace. Quantitative and semi-qualitative analysis of proteins showed a wide range among the fractions, mainly of prolamine (13.47–28.43 g Kg−1) and glutelin (5.57–30.98 g Kg−1) contents. Pixurum 6, Pixurum 5, and MPA1 landraces are of superior nutritional value for their albumin, globulin, and glutelin contents. PCA of the spectral dataset in the fingerprint region to carbohydrates (1200–950 and 1065–950 cm−1) also including commercial standards of amylose and amylopectin was able in separating the Moroti genotype, which grouped with the amylopectin standard. Thus, ATR-FTIR and PCA showed to be useful tools for the quick screening and discrimination of maize with distinct chemical composition.