This Reporting Manual provides guidance for reporting on zoonoses, zoonotic agents and antimicrobial resistance in animals, food and feed under the framework of Directive 2003/99/EC. Some advice is also given on reporting on other pathogenic microbiological agents in food. The objective is to harmonise and streamline the reporting made by the Member States in a way that the data collected would be relevant and easy to be analysed at the Community level. The manual covers all the agents and items included by the current data collection through the web-based reporting system run by the European Food Safety Authority. Detailed guidelines are provided for reporting of the data in the tables and text forms. This guidance typically applies to the agents, animal species and food categories to be reported on. Instructions are also given on description of the sampling and monitoring schemes as well as analyses of the results in the national reports. Special reference is made to fields were following of trends would be desirable. This manual is specifically aimed to guide the reporting of information deriving from the year 2009.