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<i>Fusarium</i> head blight (FHB) epidemics in wheat and contamination with <i>Fusarium</i> mycotoxins has become an increasing problem over the last decades. This prompted the need for non-invasive and non-destructive techniques to screen cereal grains for <i>Fusarium</i> infection, which is usually accompanied by mycotoxin contamination. This study tested the potential of hyperspectral imaging to monitor the infection of wheat kernels and flour with three <i>Fusarium</i> species. Kernels of two wheat varieties inoculated at anthesis with <i>F. graminearum, F. culmorum</i>, and <i>F. poae</i> were investigated. Hyperspectral images of kernels and flour were taken in the visible-near infrared (VIS-NIR) (400&#8722;1000 nm) and short-wave infrared (SWIR) (1000&#8722;2500 nm) ranges. The fungal DNA and mycotoxin contents were quantified. Spectral reflectance of <i>Fusarium</i>-damaged kernels (FDK) was significantly higher than non-inoculated ones. In contrast, spectral reflectance of flour from non-inoculated kernels was higher than that of FDK in the VIS and lower in the NIR and SWIR ranges. Spectral reflectance of kernels was positively correlated with fungal DNA and deoxynivalenol (DON) contents. In the case of the flour, this correlation exceeded <i>r</i> = &#8722;0.80 in the VIS range. Remarkable peaks of correlation appeared at 1193, 1231, 1446 to 1465, and 1742 to 2500 nm in the SWIR range.