With the continued growth of the aquaculture industry and increasing scientific discussion over the potential for negative events to give rise to suffering, research into the welfare of cultured fish is vital. How we define and measure welfare is cause for debate, particularly in fish. However, research into the effects of aquaculture procedures on welfare is crucial to produce data and recommendations for best practice and future legislation. Both behavioural and physiological measures of welfare are necessary for correct interpretation and while there is a wealth of knowledge on the physiological consequences of many aquaculture practices it is now equally important for us to understand the behavioural responses to these practices and to relate them to fish welfare. Here I review the scientific data that allows us to interpret the effects of disease, handling, transport, food deprivation, and slaughter technique on fish welfare. The effects of stocking density, also an area of welfare concern, are complex and appear to comprise of numerous interacting and case specific factors. Investigation into the relative importance of these factors, particularly through behavioural studies, will serve to improve welfare. Stocking density, diet, feeding technique, and management procedures all have strong effects on stress responses, subsequent stress tolerance, health, and the occurrence of aggressive behaviour. Strategies to reduce disease susceptibility, minimise stress responses, and avoid aggression are, therefore, vital. However, caution should be taken when interpreting ‘‘abnormal’’ fish behaviour and further research is required to allow us to establish the importance of the expression of ‘‘natural’’ behaviours. Collectively this growing area of research serves to improve our knowledge of the impacts of aquaculture and intensive farming procedures on fish welfare and is the first step in improving welfare wherever possible.