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A feasibility interlaboratory comparison (ILC) was organised by the European Commission’s (EC) Joint Research Centre (JRC) on the determination of the mass fraction of total cow’s milk protein in baked cookies. The ILC was organised to support Commission Regulation (EU) 1169/2011 on the provision of food information to consumers, including the mandatory allergen food labelling and the harmonisation of measurement procedures used for food allergen analysis. An incurred baked cookie was prepared at the JRC and samples were sent to participants for analysis. The laboratories were asked to report their results as “mass fraction of total cow’s milk protein in baked cookies”. This common well-defined measurand was used for the first time in such an ILC to assess the equivalence of measurement results. Homogeneity and stability of the test material were demonstrated to be adequate. An indicative assigned value was established using the JRC single-laboratory validated method based on liquid chromatography coupled to mass spectrometry (LC–MS), independently from the results reported by the participants. Twenty-three laboratories from the European Network of Food Allergen Detection Laboratories (ENFADL), representing 20 European Union (EU) Member States, reported results. Their laboratory performance was assessed using the percent difference Di score. The participating laboratories applied either enzyme-linked immunosorbent assays (ELISA) or LC–MS. Even though the majority of the laboratories used commercially available ELISA test kits, a significant scatter of all the reported results was observed. This indicates that further harmonisation is required for measurement procedures aiming to determine potentially allergenic constituents in food.