The European Union (EU) Summary Reports on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2009 and 2010 – specifically for the data on Salmonella, Campylobacter, verotoxigenic Escherichia coli, Listeria monocytogenes and foodborne outbreaks was reviewed. The main conclusions and recommendations are reported. Comparison between EU Member States (MSs) was found to be difficult due to the differences of the methods used, sampling schemes and reporting systems. Methods, sampling schemes and reporting systems among MSs should therefore be harmonised. When comparing MS-specific trends, the impact of sample sizes, weight of samples and methodologies should be considered, as these variables could otherwise lead to misinterpretation of the data. Incidence data alone do not provide a full picture of the public health burden of zoonotic diseases. Fatalities provide another important insight. Ultimately, summary measures of public health such as disability adjusted life years (DALYs) and cost-of-illness estimates should be presented. Travel information was found to be still incomplete in many MSs. For many pathogens this hampers source attribution. To better understand the public health problems related to food and animal sources in the EU, it is desirable to differentiate between travel within and outside the EU. This would also be useful to better evaluate the public health impact of EU-wide food safety measures. Whenever possible the data/results should be analysed using proper statistical tools. When data do not allow for this, the text should be kept to presenting the data without implying any patterns or trends.