The organisational design of a national Veterinary Service is critical to the overall quality and integrity of its animal health and veterinary public health infrastructure. It is well recognised that the diversity of political, economic and social situations which exist in and between countries dictates that no one model of organisational structure can be applied to all circumstances. In Canada, a re-organisation of the approach of the federal government to food inspection in 1997 resulted in the transfer of the veterinary administration to a newly created agency called the Canadian Food Inspection Agency (CFIA). The authors provide a short background on the impetus for the creation of the CFIA and an overview of its organisational structure and responsibilities in animal and veterinary public health and food safety. Also included are the logic models that were developed for the federal Veterinary Services as part of their quality and performance management framework. Integrating all federally mandated food inspection systems under the CFIA has had concrete benefits in clarifying roles and responsibilities, reducing overlap and duplication of programme functions, improving service delivery and facilitating federal-provincial collaboration. Moreover, the strength of the organisation lies in the ability of the Canadian Veterinary Services to adhere to the fundamental principles of quality which are recommended by the OIE (World organisation for animal health) for the evaluation of Veterinary Services. No single organisational structure can guarantee a highly effective or competent Veterinary Service. Common challenges exist that may or may not be addressed in whole or in part by the organisational structure. The challenges highlighted in this paper provide further thoughts on the management of shared jurisdiction, meeting public health objectives, balancing science and political accountability, and defining the role and jurisdiction of veterinarians.