The dramatic intensification and diversification of global aquaculture has made aquaculture an important food-producing sector, providing an essential source of aquatic protein for a growing human population. The sector is recognised as creator of jobs and an important source of foreign export earnings for both developed and developing countries. However, the expanded global movements of live aquatic animals have been accompanied by the transboundary spread of a wide variety of pathogens necessitating the routine use of veterinary medicines to prevent and treat disease outbreaks, assure healthy stocks and maximise production. The use of appropriate antimicrobial treatments is one of the most effective management responses to such emergencies, but their inappropriate use can lead to increased frequency of bacterial resistance, potential transfer of resistance genes in bacteria from the aquatic environment to other bacteria, and the occurrence of bacterial residues in aquaculture products resulting in bans by importing countries. The FAO/AAHRI Expert Workshop on Improving Biosecurity through Prudent and Responsible Use of Veterinary Medicines in Aquatic Food Production was convened in Bangkok, Thailand, from 15 to 18 December 2009, to understand the current status of the use of antimicrobials in aquaculture, and to discuss the concerns and impacts of their irresponsible use on human health, the aquatic environment and trade. The discussions became the basis for drafting recommendations targeted at government and private sectors, and for developing guiding principles on the responsible use of antimicrobials in aquaculture to be considered as part of future FAO Code of Conduct for Responsible Fisheries (CCRF) Technical Guidelines for Responsible Fisheries on Prudent and Responsible Use of Veterinary Medicines in Aquaculture. Part 1 of this publication contains 15 technical background papers presented during the expert workshop, contributed by 29 specialists. Part 2 contains the highlights of the expert workshop. Because aquaculture is expected to continue to increase its contribution to the world's production of aquatic food, offer opportunities to alleviate poverty, increase employment and community development, and reduce overexploitation of natural aquatic resources, appropriate guidance to aquaculture stakeholders on the responsible use of veterinary medicines has become essential. Safe and effective veterinary medicines need to be available for efficient aquaculture production, and their use should be in line with established principles on prudent use to safeguard public and animal health. The use of such medicines should be part of national and on-farm biosecurity plans and in accordance with an overall national policy for sustainable aquaculture.