We estimated the true incidence of campylobacteriosis and salmonellosis in the European Union (EU) in 2009. The estimate was based on disease risks of returning Swedish travellers, averaged over the years 2005-2009, and anchored to a Dutch population-based study on incidence and aetiology of gastroenteritis. For the 27 EU member states the incidence of campylobacteriosis was about 9.2 (95 % CI 2.8-23) million cases, while the incidence of salmonellosis was 6.2 (95 % CI 1.0-19) million cases. Only 1/47 (95 % CI 14-117) cases of campylobacteriosis and one 1/58 (95 % CI 9-172) cases of salmonellosis were reported in the EU. The incidence rate of campylobacteriosis in EU member states varied between 30 and 13 500/100 000 population and was significantly correlated with the prevalence of Campylobacter spp. in broiler chickens. The incidence rate of salmonellosis in EU member states varied between 16 and 11 800/100 000 population and was significantly correlated with the prevalence of Salmonella Enteritidis in laying hens.