In this work, theoretical and experimental infrared spectra of fatty acid methyl esters (FAME) contained in soybean biodiesel were analyzed seeking the assignments of the relevant vibrational modes to characterize crude soybean oil and soybean biodiesel. The results showed the usefulness of infrared spectra for monitoring saturated and unsaturated compounds as well as impurities (mainly glycerol) in raw samples. This is the first step toward proposing an efficient molecular spectroscopy routine to certify biodiesel fuel.