The purpose of this study was to investigate the feasibility of using Fourier transform mid-infrared (FT-IR) microspectroscopy, with attenuated total reflectance (ATR), to detect the presence of Fusarium spp., classify differences in ability to detect Fusarium spp. among the Canadian soil zones, determine whether Fusarium spp. can serve as an indicator for the concentration of deoxynivalenol (DON), and develop an equation that can predict DON within wheat kernels. Canadian Western Red Spring wheat kernels were pressed against an ATR crystal to obtain spectra. Five chemical functional groups were investigated. The ability of FT-IR-ATR microspectroscopy to detect the presence of Fusarium spp. was confirmed. The chemical composition, and the ability to identify Fusarium spp., differed in kernels grown among the soil zones. Several methods to use Fusarium spp. as an indicator for the concentration of DON content within the wheat kernels were attempted and found to be unsuccessful.