The concern regarding toxicity from the presence of deoxynivalenol (DON) in wheat that affects both economy and public health leads to the need to find appropriate detection methods for determining the degree of DON contamination in terms of the equipment available and the speed required for obtaining the incidence. The objective of this study was to compare the performance of two alternative analytical techniques for DON quantification for use in the food industry with a reference technique. Samples of wheat and the commercial by-products were analysed by high-performance liquid chromatography (HPLC) with an ultraviolet detector as the reference method and the results compared with those obtained from a rapid lateral-flow immunochromatographic device (Reveal Q+) and of a Fourier-transform-infrared (FTIR) spectroscopy technique. Pearson’s correlation coefficient between the HPLC and Reveal-Q+ data (0.45), although significant (P<0.0003), was lower than that obtained between HPLC and the FTIR method (0.94, P<0.0001). Both methods were considered efficient in quantifying DON levels in wheat-flour samples. This study was aimed at assisting the producers in choosing an appropriate tool for the purpose of analysis and upon consideration of the available equipment.