A European Union-wide baseline survey on methicillin-resistant Staphylococcus aureus (MRSA) was conducted in 2008 in holdings with breeding pigs. A total of 1,600 holdings housing and selling mainly breeding pigs (breeding holdings), and 3,473 holdings housing breeding pigs and selling mainly pigs for fattening or slaughter (production holdings) from 24 Member States and two other European countries were included in the survey. Pooled dust samples collected from holdings were tested for MRSA. The likelihood of a limited set of holding-level factors to be potentially associated with MRSA-positive holdings were analysed by multiple regression analysis, separately for breeding and for production holdings. These analyses showed that the risk of holdings of being contaminated with MRSA increased as the number of breeding pigs in the holding increased, in both breeding and production holdings. Analyses at country-level demonstrated a strong positive association between the prevalence of MRSA-positive breeding holdings and MRSA-positive production holdings, suggesting a vertical dissemination of MRSA between the holdings. A complementary country-level analysis using TRAde Control and Expert System data on intra-Community trade further disclosed strong positive associations between the prevalence of MRSA-positive holdings with breeding pigs and the volume of imported breeding pigs, and a proxy for numbers of imported breeding pigs at risk of being colonised with MRSA. Further investigation of the diversity of MRSA Staphylococcus protein A types (spa-types) showed that the distribution of spa-types differed significantly between countries. Spa-types belonging to lineages MRSA ST1, ST5, and ST8 tested negative for Panton-Valentine leukocidin (PVL) toxin genes, suggesting that these strains were not related to the PVL-positive MRSA strains known in human medicine. Further investigations of risk factors for MRSA holding contamination at country level, as well as investigations on prevention and intervention measures to contain MRSA contamination in pig holdings are recommended.