The Treaty of Amsterdam, in force since 1 May 1999, has established new ground rules for the actions of the European Union (EU) on animal welfare. It recognizes that animals are sentient beings and obliges the European Institutions to pay full regard to the welfare requirements of animals when formulating and implementing Community legislation. In order to properly address welfare issues, these need to be assessed in a scientific and transparent way. The principles of risk assessment in terms of transparency and use of available scientific data are probably well suited for this area. The application of risk assessment for terrestrial and aquatic animal welfare is a relatively new area. This paper describes the work developed in the context of the European Food Safety Authority (EFSA) opinions on the application of a risk assessment methodology to fish welfare. Risk assessment is a scientifically based process that seeks to determine the likelihood and consequences of an adverse event, which is referred to as a hazard. It generally consists of the following steps: (i) hazard identification, (ii) hazard characterisation, (iii) exposure assessment and (iv) risk characterisation. Different approaches can be used for risk assessments, such as qualitative, semi-quantitative and quantitative approaches. These are discussed in the context of fish welfare, using examples from assessments done to aquaculture husbandry systems and stunning/killing methods for farmed fish. A critical review of the applications and limitations of the risk methodology in fish welfare is given. There is a need to develop appropriate indicators of fish welfare. Yet, risk assessment methodology provides a transparent approach to identify significant hazards and support recommendations for improved welfare.