Contamination of cereals and related products with Fusarium toxins causes feed-borne intoxication especially in farm animals. Therefore, efficient analytical tools for qualitative analysis and quantitation of fungal metabolites in feed are required. Methods usually include an exhaustive extraction, a clean-up step to reduce or eliminate unwanted matrix components and a separation and detection step. Currently, quantitative methods of analysis for most Fusarium toxins use immunoaffinity clean-up with high performance liquid chromatography (HPLC) or gas chromatography (GC) in combination with a variety of detectors. Screening of samples contaminated with mycotoxins is frequently performed by thin layer chromatography (TLC) and yields qualitative or semi-quantitative results. More recently, enzyme-linked immunosorbent assays (ELISA) are often used for rapid screening. A number of emerging methods such as fluorescence polarization immunoassays, dipsticks, or even newer methods such as biosensors and non-invasive methods based on infrared and acoustic techniques have shown great potential for mycotoxin analysis. Currently, there is a trend towards developing multimycotoxin methods for the simultaneous analysis of several Fusarium mycotoxins belonging to different chemical families which is best achieved by LC-MS/MS (liquid chromatography with tandem mass spectrometry). The current paper gives an overview of the currently used methodology for the analysis of the Fusarium toxins fumonisins (FBs), moniliformin (MON), zearalenone (ZON) and type-A and -B trichothecenes in feeds, as well as other essential issues in mycotoxin analysis such as the availability of reliable calibrants and reference materials