Metals, PCBs and pesticides were measured in various organs of 13 deep water fish species caught between 80 and 4000m depth in 5 locations in the eastern North Atlantic and one in the eastern South Atlantic. The results were investigated in relation to biological and environmental factors. The levels of metals and organic contaminants in muscle tissue were generally below the EU regulatory limits for food, although up to 10% of individuals were above. Livers were not suitable for human consumption and, with the forthcoming EU regulations on PCBs and dioxins, will not be suitable as fish oil or fish meal either. Metal levels in deep water fish were similar to those in shallow water fish, apart from Cu, Cd and Hg, which were higher. Levels were similar in both hemispheres, but differences between areas were found. Top predators, benthic feeders and species below 2000m depth were more contaminated. The preferred organ of accumulation of each metal as well as correlations with depth were species dependent. Hg and Cd were positively correlated with length, showing bioaccumulation, whilst As was negatively correlated with length as it is adsorbed from the gills rather than food. Organic contaminants were evenly distributed throughout the body's lipids, by equilibrium with the concentrations in the surrounding water. Inter-species differences were attributed to differences in phospholipid compositions. Levels of organic contaminants were substantially lower in the southern hemisphere. Compared to shallow water fish, deep water species presented an increased burden of p,p'-DDT, due to their lesser ability to metabolise this compound; and of higher chlorinated biphenyls, due to selective transport to the deep sea. Differences between water masses were visible from the HCH isomer composition. PCB concentrations presented a seesaw pattern with the log of the octanol-water coefficient rather than a linear relationship, which was attributed to the specific steric effect of each congener.