Due to the growing demand for rapid, sensitive and inexpensive detection of contaminations in food and feed, both in the field and after harvest, non-invasive and non-destructive spectroscopic methods are reviewed for the direct identification of fungi and mycotoxins on grain and in grain products. Different model samples containing defined contaminations of fungi and/or mycotoxins as well as real-world samples were investigated using spectroscopic methods (steady-state and time-resolved fluorescence spectroscopy, ultraviolet/visible/near infrared (NIR) spectroscopy, two-photon-induced fluorescence (TPIF)). To evaluate the capability of TPIF for on-line and in-line mycotoxin analysis in real-world samples, fundamental parameters of different mycotoxins, such as two-photon cross-sections, were determined in beer and wine. A comparison showed that the disturbance due to background emission originating from matrix constituents is significantly reduced under twophoton excitation conditions, and TPIF can be applied for a qualitative and quantitative analysis of mycotoxins in wine and beer. The combination of data obtained from different spectroscopic methods (such as optimised excitation and emission wavelengths, fluorescence decay times and fluorescence quantum efficiency on the one hand side and NIR spectroscopy on the other side) is promising for the qualitative as well as quantitative identification of fungi and mycotoxins. Moreover, NIR reflection spectra yield additional information on ingredients, moisture content and the presence (or absence) of fungi in the sample. The spectroscopic techniques are complemented by chemometric tools to extract the desired chemical information, e.g. with respect to the presence of contaminations.