As Salmonella is one of the major causes of food-borne disease in the European Union (EU), EU approved legislation to achieve a reduction of the prevalence of this agent in the pig sector. To set the target for this reduction in each country it was decided to carry out baseline surveys in the EU to estimate the prevalence of the agent. The dataset analyzed in this work refers to the cross sectional baseline survey on the prevalence of Salmonella in breeding pigs in Portugal. A total of 1670 pen fecal samples from 167 herds were submitted to fecal culture.