In this report, proposals to improve the harmonisation of monitoring of prevalence, genetic diversity and antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA)from food-producing animals and food derived thereof by the European Union Member States are presented. The primary route of zoonotic transmission of MRSA is considered to be the direct or indirect occupational contact of livestock professionals with colonised animals, while the role of food as a source of human colonisation or infection is presently considered to be low. Sampling recommendations have therefore prioritised several different food-producing animal populations previously described as MRSA reservoirs and, to a lesser extent, food produced by these animals. Monitoring in primary production, including at slaughter, is pivotal because of the main transmission route, while additional monitoring in food may help with the assessment of consumers’ exposure via this route. A consistent monitoring in broiler flocks, fattening pigs and dairy cattle, as well as in veal calves under 1 year of age and fattening turkey flocks, in those countries where production exceeds 10 million tonnes slaughtered/year, is recommended every third year on a rotating basis. It is proposed that breeding poultry flocks and breeding pigs, as well as meat and raw milk products, are monitored on a voluntary basis. Representative sampling should be made within the framework of the national Salmonella control programmes for the poultry populations targeted, at the slaughterhouse for calves and either on farm or at the slaughterhouse for fattening pigs. Harmonised analytical methodologies for identification, typing and further characterisation of MRSA are proposed. The use of the microdilution method applied to a harmonised set of antimicrobials, and interpreted using EUCAST epidemiological cut-off values for antimicrobial susceptibility testing of MRSA, is recommended. Finally, full support is given to collection and reporting of isolate-based data, in particular to enable analysis of multi-resistance.