The inter-laboratory (=ring-trial) validation of 4 food allergen quantification methods using real-time PCR is described. Three single real-time PCR methods for the specific detection and quantification of sesame, almond and Brazil nut were used. Additionally, a multiplex real-time PCR method combining the detection of sesame, almond, Brazil nut and lupine was tested in parallel. Matrix based calibrants (rice cookies) spiked (=incurred) with defined amounts of sesame, almond, lupine and Brazil nut were applied for quantitative evaluation. Cookies based upon wheat and rice flour as well as sauce hollandaise powder each incurred with these allergenic ingredients in the range of 10–123 milligram per kilogram were used as ring-trial samples. The lowest spike level of 10 mg/kg could reproducibly be detected by 6 of 7 PCR systems. In quantitative evaluation of the results, reproducibility standard deviations of approximately 50 % and below were obtained. In addition, the effect of the food matrix on allergen quantification was examined. The range of “recoveries” over all matrices and methods was from 43 to 109 %.