Animal diseases remain one of the main problems for livestock production in terms of trade development, poverty reduction and public health. Animal health systems are complex because of the diversity of the parties involved and because of various changes in the delivery of veterinary services, such as the redefinition of the roles of the public and private sectors. It is, therefore, often difficult to assess the global performance of animal health systems and sub-systems in terms of their medical, economic and social effectiveness. In addition, the necessary reliability of the health information obtained leads to certification of the status of regions and countries with regard to epizootics, which requires a high degree of standardisation and conformity with international norms. An assessment therefore needs to be made of the advantages of alternative systems compared with conventional systems. An animal health system should be seen as a whole, and when assessing its overall performance several things must be taken into account, e.g. the markets for products and the sometimes contradictory interests of all the different parties involved. There are, therefore, many research needs and avenues to be pursued, including: – the methods, data and tools required for assessing the effectiveness of systems, including a definition of what constitutes a reliable indicator – the factors that determine the health of a herd; having a clearer idea of what will affect herd health will make it possible to map risk indicators and animal health care needs – the design and management of realistic and harmonised animal health information systems whose indicators provide reliable measurements of health – the function, organisation and effectiveness of participative surveillance approaches – the definition and effectiveness of animal health contracts, such as health mandates between the State and private veterinarians – the function and role of livestock auxiliaries – the establishment of assessment methods and standards that take into account the specific situation of southern countries that could lead to the certification and accreditation of alternative systems. The efficiency of these systems must then be tested (direct impact, cost-benefit studies) using the above-mentioned indicators, and an implementation ‘toolkit’ can then be assembled, taking into account the local differences which will affect the suitability of each system for different locations. Research into the assessment of animal health systems is a long-term investment, but it ensures that quality certification is reliable and allows for the safe development of animal product markets.