Affinity column clean-up of food samples for mycotoxin analysis produces extracts which are free of co-extractives and therefore require little chromatography for separation and quantification of the target analytes. Using such clean extracts, we report rapid chromatographic methods for aflatoxins B(1), B(2), G(1) and G(2), aflatoxin M(1), ochratoxin A, zearalenone and fumonisins. Using short columns with small particle size packing, HPLC conditions have been developed reducing analysis time typically by 75%, e.g. for aflatoxins from 19.0 mm to 4.0 min with full separation of the four toxins and for aflatoxin M(1) giving an analysis time of less than 1 min compared to 5 min for conventional analysis. Fumonisins were analysed directly by LC/MS in a run time of 4.1 min, using selected ion monitoring to avoid the need for derivatisation for fluorescence detection by HPLC. Peak purity under rapid analysis conditions has been demonstrated by LC/MS for a variety of food extracts such as pistachios, hazelnuts, paprika, cocoa, coffee, cereals, sesame oil, cheese, maize, animal feed, dried figs, dried vine fruits, cornflakes and bread. These substantial reductions in analysis time offer significant benefits to laboratories undertaking routine screening and quantitative analysis of mycotoxins in foods.