Technical specifications are proposed for the monitoring of temporal trends in zoonotic agents in animal and food populations at Community or Member State group level in the framework of Directive 2003/99/EC. Two types of trend monitoring are identified: trend watching, which covers general observations of harmonised or non-harmonised data for possible trends, and trend analyses which means statistical analyses of harmonised data for the detection of trends over time. Trend watching can be regarded as the first and preliminary step in trend monitoring. The specifications identify a set of criteria for the selection of the zoonotic agent/animal or food category combinations where trend analyses would be justified. Based on data available from 2004 to 2007, the following combinations are suggested for trend analyses: Salmonella in fresh broiler and pig meat, flocks of laying hens and broilers, slaughter and breeding pigs as well as fattening turkeys; Campylobacter in fresh broiler meat; Listeria monocytogenes in smoked fish; Mycobacterium bovis in bovine herds; Brucella in bovine and caprine/ovine herds in co-financed non-officially free Member States; verotoxigenic Escherichia coli O157 in cattle; and Echinococcus multilocularis in red foxes. This list is proposed to be revised on a regular basis taking into account most recent knowledge. Suggestions for minimum sample sizes and number of time points needed for identifying trends are provided. Weighting of the national results should be applied at Community level in order to account for the different sizes of national populations. Biological relevance of trends depends on several factors such as the prevalence of the agent in the population, and the severity of the disease in question, as well as on the impact of the trend on the exposure to humans. Statistical significance of a trend observed in data is therefore only one of the factors impacting on the biological relevance of an observed trend.