The possibility of using two Fourier transform mid-infrared spectroscopic techniques was investigated with the purpose of rapid detection of mycotoxin-producing Fusarium fungi on wheat, as an indicator for the presence of the mycotoxin deoxynivalenol (DON). Samples of a single wheat genotype (Monika, blanks and contaminated with Fusarium graminearum) were ground and analyzed applying the diffuse reflection (DR) and attenuated total reflection (ATR) modes. The recorded spectra were evaluated with principal component analysis and the blank and contaminated samples were classified by cluster analysis. Besides, the possibility was examined of determining DON on the basis of the ratio of ATR signals at 1709 cm– 1 and 1743 cm– 1. Reference measurements were performed by high performance liquid chromatography with diode array detection. The concentration range for contaminated samples was 2.51– 12.14 mg/kg. Classification efficiency was 100% for ATR spectra, whereas DR spectra did not show so obvious clustering of contaminated and blank samples. The ATR technique appeared advantageous owing to its easier use and interpretation of results, which were better in respect of classification and quantification. Quantification using partial least squares (PLS1) regression, as well as multiple linear regression (MLR) showed good correlation with DON reference data for the mentioned wheat genotype.