The aim of this study was to gather information on current animal welfare practices in European aquaculture as regards the transport and slaughter of farmed fish, and to analyse the extent that fish welfare issues remain unresolved. The costs of adhering to good welfare practices, the economic situation, effects on competitiveness and other factors were taken into account. The reference period was 2009-2013. The study focused on the five main farmed fish species to provide a general presentation of the current situation in European aquaculture: Atlantic salmon (cold-water marine); common carp and rainbow trout (freshwater), and; European sea bass and gilthead sea bream (Mediterranean marine). The international standards of the World Organisation for Animal Health (OIE) on animal welfare during transport and stunning and killing of farmed fish for human consumption were used as a benchmark for assessment of welfare practices. EFSA recommendations on slaughter were also taken into account