Mycotoxins are secondary metabolites of fungi poisonous for humans or animals which can be found on a great variety of food and feed commodities. Food is not necessarily safe just because the presence of well-known mycotoxins has been ruled out, as they might still be there in disguise. Mycotoxins may also occur in conjugated form, either soluble (masked mycotoxins) or incorporated into/associated with/attached to macromolecules (bound mycotoxins). These conjugated mycotoxins can emerge after metabolization by living plants, fungi and mammals or after food processing. Awareness of such altered forms of mycotoxins is increasing, but reliable analytical methods, measurement standards and occurrence and toxicity data are still lacking. In this paper currently known conjugated mycotoxins, their formation and determination are reviewed. For the latter, liquid chromatography-(tandem) mass spectrometry or ELISA methods are employed with or without conversion to the parent mycotoxins. Sample preparation to transform the bound forms into soluble forms can involve enzymatic or acidic/alkaline treatment. Especially mycotoxins which are in contact with living plants in the field are prone to be metabolized. This transformation process is not only important regarding food safety but also for the resistance of plants towards fungal-induced diseases, such as Fusarium head blight of wheat.