In the last decade, near-infrared (NIR) and mid-infrared (MIR) spectroscopy have proven to be most promising tools for the detection of fungal contamination and estimation of mycotoxins in agricultural commodities, particularly of cereals. Owing to significant economic losses incurred from fungal contamination of foodstuffs, producers and processors are looking for fast, reliable, and less-expensive methods for the detection of fungal damage. In this context, NIR and MIR spectroscopy offer a fast, less-expensive, non-destructive, and relatively simple analytical method. Results from published studies indicate that NIR and MIR spectroscopy can be successfully applied to identifying fungal contamination and estimating specific mycotoxins. This review will focus on the applications of NIR and MIR spectroscopy to the classification of fungal contamination and the determination of specific mycotoxin contamination levels, and to compare this technology with traditional analytical methods.