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Mycotoxins, which are toxins produced by fungi, can pose great danger to human health with their acute and chronic effects when contaminated foods (grains, fruits, meat, or milk) are ingested. Fungal infections in food crops are extremely common and many developed countries have set standards to monitor and control their imported and exported food products. The analytical methods required to quantify the toxin concentrations are accurate and sensitive but often destructive thus rely on sampling to determine the contamination status. Infrared spectroscopy has gained a lot of attention for its ability to non-destructively provide critical information of samples, which can help reduce the uncertainties inherited from the sampling methods. Several successful examples in identifying fungal infection from agricultural commodities provide great hope for a faster and more cost-effective screening method to help eliminate the health threats.