Abstract Infections of wheat, rye, oat and barley by Fusarium ssp. are serious problems worldwide due to the mycotoxins, potentially produced by the fungi. In 2005, limit values were issued by the EU commission to avoid health risks by mycotoxins, both for humans and animals. This increased the need to develop tools for early detection of infections. Occurrence of Fusarium-caused head blight disease can be detected by spectral analysis (400–1000 nm) before harvest. With this information, farmers could recognize Fusarium contaminations. They could, therefore, harvest the grains separately and supply it to other utilizations, if applicable. In the present study, wheat plants were analyzed using a hyper-spectral imaging system under laboratory conditions. Principal component analysis (PCA) was applied to differentiate spectra of diseased and healthy ear tissues in the wavelength ranges of 500–533 nm, 560–675 nm, 682–733 nm and 927–931 nm, respectively. Head blight could be successfully recognized during the development stages (BBCH-stages) 71–85. However, the best time for disease determination was at the beginning of medium milk stage (BBCH 75). Just after start of flowering (BBCH 65) and, again, in the fully ripe stage (BBCH 89), distinction by spectral analysis is impossible. With the imaging analysis method ‘Spectral Angle Mapper’ (SAM) the degree of disease was correctly classified (87%) considering an error of visual rating of 10%. However, SAM is time-consuming. It involves both the analysis of all spectral bands and the setup of reference spectra for classification. The application of specific spectral sub-ranges is a very promising alternative. The derived head blight index (HBI), which uses spectral differences in the ranges of 665–675 nm and 550–560 nm, can be a suitable outdoor classification method for the recognition of head blight. In these experiments, mean hit rates were 67% during the whole study period (BBCH 65–89). However, if only the optimal classification time is considered, the accuracy of detection can be largely increased.