Modified mycotoxins formed by plants, fungi and during some food processing steps may remain undetected by analytical methods, potentially causing underestimation of mycotoxin exposure and risk. Furthermore, due to altered physico-chemical characteristics of modified mycotoxins, these compounds might have different gastro-intestinal absorption compared to the unmodified forms, leading to altered modified mycotoxin plasma concentrations. Additionally, modified mycotoxins can be converted back into their corresponding unmodified forms by in vivo hydrolysis upon oral ingestion. This review aims to describe the current knowledge on the production, occurrence, toxicity and toxicokinetic properties of the modified Fusarium mycotoxins. The need for more occurrence data to correctly assess the risks associated with these modified mycotoxins is clearly indicated, including differences between commodities as well as geographical and climatological influences. Research on toxicity of these modified forms demonstrates the possibility of significant decreases as well as increases in the toxic effects of these compounds compared with those of the unmodified forms. Their toxicokinetics demonstrates that a decreased (increased) polarity of modified mycotoxins might cause enhanced (decreased) oral absorption. The possibility of in vivo hydrolysis, altered toxicity and their wide-spread occurrence makes modified mycotoxins a complex threat for which a risk assessment will require prospective multi-disciplinary efforts.