A European Union-wide Salmonella baseline survey was conducted in 2008 in holdings with breeding pigs. A total of 1,609 randomly selected holdings housing and selling mainly breeding pigs (breeding holdings) and 3,508 holdings housing commercial breeding pigs and mainly selling pigs for fattening or slaughter (production holdings) were sampled. In each selected holding, pooled fresh faecal samples were collected from 10 randomly chosen pens of breeding pigs over six months of age, representing the different stages of the breeding herd, and examined for the presence of Salmonella. Analyses at country-level demonstrated a strong positive association between the prevalence of Salmonella-positive breeding holdings and the prevalence of Salmonella-positive production holdings, suggesting a vertical dissemination of Salmonella between the holdings. Based on the combined results from breeding and production holdings, multivariable regression analysis showed that the odds of Salmonella-positive pens with pigs increased with the number of breeding pigs in the holding and with the following pen-level factors: flooring systems other than slatted floors or solid floors with straw, presence of maiden gilts, number of pigs per pen, feed of commercial compound origin or pelleted feed. A tendency towards some Member State group-specific Salmonella serovars was identified, but spatial distribution of other serovars was heterogeneous. S. Typhimurium and S. Derby were widespread and dominant in the EU, in both breeding and production holdings. However, many other serovars were relatively prevalent in Western EU Member States. A complementary within-holding prevalence study indicated that, due to a non-perfect diagnostic test sensitivity, the observed EU-level prevalence of Salmonella-positive holdings with breeding pigs was roughly 80% of the estimated true EU-level prevalence. But this proportion varied between Member States.