To assess the impact of foodborne diseases and non-foodborne zoonoses on human health and to establish priorities for the surveillance, prevention, and control of these diseases, the French Institute for Public Health Surveillance coordinated two studies using different methodologies: one defining priorities in the field of non-foodborne zoonoses in 2000–2001 and the other examining morbidity and mortality due to foodborne infectious diseases in France during the 1990s. The first study involved a prioritization process for non-foodborne zoonoses based on an analysis by a group of experts in human and veterinary public health. This analysis included group discussions, individual assessments, and consultation with external experts when necessary. For the second study, the number of infection cases, hospitalizations, and deaths was estimated for 23 pathogens based on the various available data sources identified. For each pathogen studied, several point estimates were obtained using a method adapted to the nature of the data from each source and the pathogen under study. The estimates considered most plausible—based on an understanding of how the various data sources function and their content, comparison with foreign data, and expert opinion—were selected and presented as a plausible range with lower and upper bounds.