The European Commission asked the Scientific Panel on Biological Hazards of the European Food Safety Authority to consider the Food Safety aspects of animal welfare of husbandry systems for several species of fish farmed in the EU. In this opinion, the BIOHAZ Panel has focused on the food safety relevance of pre-harvest factors relating to fish welfare, in one opinion incorporating aspects regarding six species (Atlantic salmon, gilthead sea bream, sea bass, trout species, carp species and European eel). Only biological risks have been assessed, as consideration of the occurrence and principles of control of chemical residues (including mycotoxins and marine toxins) in farm animals is outside the mandate of the BIOHAZ panel. Farm location, the species being farmed, husbandry practices and environmental conditions are all factors that influence the food safety risk associated with aquaculture products. Risk is also influenced by post-harvest processing and practices and habits in food preparation and consumption. A major advantage of aquaculture in regard to food safety is that control can be exerted over the quality and safety of the product, and many of the hazards at the production level can be controlled by good aquaculture practices and safety management systems. Specific information on the effect of welfare-related pre-harvest practices that may affect fish safety is scarce and knowledge gaps on the issues of fish welfare and their influence on food safety abound. Hence only general considerations of relationships or effects identified, based on general principles of hygiene and safety, are presented in this opinion. As far as location is concerned, European farms are located in sub-arctic and temperate waters in coastal, brackishwater, and in inland freshwater habitats, with generally low levels of pathogenic microorganisms and parasites as compared to other latitudes. The European aquaculture industry commonly implements fish health management and pre-harvest quality and safety control measures, contributing to a significant reduction of risks associated with biological hazards and, at the same time, achieving a high degree of control over the production process. Risks can be additionally controlled by hygienic processing and post-processing, preparation of foods and appropriate habits of food consumption. Production procedures based on good aquaculture practices (as recommended in different industry codes of practice) that result in provision of optimal animal welfare increase fish resistance to infections and therefore may lead to a reduction of the food safety risks associated with the resulting end products. Measures intended to maintain fish welfare by avoiding stress or improving environmental conditions are expected to have a positive impact on the safety of the food product. Environmental and hygienic conditions (related to water temperature, salinity, chemicals, organic matter, oxygen levels, etc.) and practices at pre-harvest level (inadequate feeding or antimicrobial usage), could increase the prevalence of certain biological hazards at farm level, and may also have an effect on fish welfare and physiological condition (stress). Both these aspects impact on fish health, and subsequently may influence the safety of the end product. Some aquaculture practices and conditions inherent to specific production methods may influence the safety of the food product. Intensive systems give producers a better opportunity to manage biological risks by using water and feed quality control, biosecurity, health management, and vaccination. On the other hand, some conditions (mostly associated with handling and crowding) occur more commonly in intensive systems and, if not properly managed, they may act as stressors, increasing the risk of pathogen carriage and disease. Extensive systems have a lower degree of intensification and avoid excessive handling and crowding, therefore, are in principle less stressful. On the other hand, and when control can not be fully exerted over risk factors (such as non-optimal feeding, poor water quality and poor fish health), there are more opportunities for pathogen carriage and disease. In all cases, pre-harvest measures are to be complemented by the best practices at the post-harvest level. Extension of coordinated animal welfare / food safety research programs should be encouraged in order to improve the desired synergism between the two approaches.