Traditionally mycotoxins are mainly determined by immunoassay screening methods or by single compound chromatographic analytical methods, based on immunoaffinity column cleanup followed by a separation step using thin layer chromatography (TLC), gas chromatography (GC) or liquid chromatography (LC), which were coupled to conventional detectors such as electron capture detection (ECD), fluorescence or UV-visible detection. In some cases, especially when fluorescence detection was used, it was necessary to include a pre- or post-column derivatisation step in order to increase the detection capabilities of the analytical method. However, the application of hyphenated chromatographic techniques, especially LC coupled to mass spectrometry (MS) and LC-MS/MS, has several advantages including simple treatment, due to further clean up procedures with immunoaffinity columns can be avoided, rapid determination and high sensitivity.