Abstract The objective was to evaluate industrial and research slaughter methods for Atlantic salmon (Salmo salar), gilt-head seabream (Sparus auratus) and eel (Anguilla anguilla) with respect to welfare and quality. As a general term of reference, an optimal slaughter method should render fish unconscious until death without avoidable excitement, pain or suffering prior to killing. For Atlantic salmon, commercial slaughter methods (carbon dioxide stunning followed by gill cutting, and gill cutting alone) are not in conformity with the general term of reference, as the fish are not rendered unconscious immediately and possibly experience stress. Evaluation of automated percussive stunning remained unconclusive. More research should enable us to ascertain whether loss of consciousness is instantaneous. Electrical stunning can be humane if applied properly. However, because flesh of electrostunned fish was characterized by occasional bloodspots, optimization of the electrical parameters is required. Prototypes for percussive and electrical stunning of salmon have been recently developed. This implies that humane slaughter of salmon is feasible for industry. For gilt-head seabream, neither aphyxia in air nor transfer of the fish to an ice slurry were considered to be humane: the methods did not induce immediate brain dysfunction and vigorous attempts to escape occurred. Percussive and electrical stunning can be in conformity with the general term of reference. However, conditions for stunning whole batches of seabream have not been established. Quality of the fish slaughtered by percussive stunning was similar to that obtained by the industrial method, i.e. immersion in an ice slurry. Further work is required to establish optimal stunning conditions and to develop prototypes. For eel, desliming in a salt-bath followed by evisceration, electrical stunning performed under the conditions prescribed by the German legislation, and live chilling and freezing were not considered to be humane. In contrast, it was established that a 10–20 kg batch of eels in fresh water could be rendered unconscious immediately and until death by applying electricity in combination with nitrogen gas. The conditions used were 0.64 A dm−2 for 1 s, followed by 0.17 A dm−2 combined with nitrogen flushing for 5 min. A preliminary assessment of flesh quality suggests that it may be improved by application of the latter method, compared with the salt bath. The results clearly indicated that humane slaughter of eels is possible in practice.