The aim of this study was to elucidate the applicability of different analytical methods for the quantitation of ergot alkaloids in rye-containing bread by means of a multi-laboratory study, and to clarify how processing of rye flour into bread affects the content of ergot alkaloids at different processing stages. Wholegrain and refined rye flours were spiked to an ergot alkaloid concentration of 500 µg/kg with ergot powder and then processed into mixed rye/wheat and wholegrain rye breads. Twelve ergot alkaloids were quantitated in flour, dough, and bread by means of liquid chromatography–fluorescence detection and liquid chromatography-tandem mass spectrometry. The effect of sample drying on the ergot alkaloid concentration was also studied. The study was carried out by two laboratories; selected bread samples were additionally analysed by two further laboratories. Both laboratories and analytical methods yielded reliable results with standard deviations of 8–9 % with spiked rye flours. Short-time dough fermentation had no effect on the recoveries. Independent of the analytical method, the bread recoveries were between 42 and 109 %, showing high measurement uncertainty of up to 40 %, which was due to both a non-standardised analytical method and the calculation of the total ergot alkaloid content from 12 individual alkaloid concentrations. Air- or freeze-drying of samples prior to analysis led to partly low recoveries. In conclusion, the study showed that there is an urgent need for a standardised analytical method for the quantitation of ergot alkaloids content in baked goods to enable the reliable control of legal thresholds.