Mycotoxins are secondary metabolites produced by toxigenic fungi in crops worldwide. In (micro)organisms such as plants, fungi, bacteria, or animals they may be further metabolised and modified, but this is also true for food processing, which may lead to a wide range of masked mycotoxin forms. These often remain undetected by analytical methods and are the culprits for underestimates in risk assessments. Furthermore, once ingested, modified mycotoxins can convert back to their parent forms. This concern has raised the need for analytical methods that can detect and quantify modified mycotoxins as essential for accurate risk assessment. The promising answer is liquid chromatography-mass spectrometry. New masked mycotoxin forms are now successfully detected by iontrap, time-of-flight, or high-resolution orbitrap mass spectrometers. However, the toxicological relevance of modified mycotoxins has not been fully clarified.