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Because of their unusual life cycle, American and European eels (Anguilla rostrata Lesueur and A. anguilla L.), are particularly exposed to pollutant effects. Because silver eels fast when they leave the freshwater system, the transoceanic migration forces them to constitute energy reserves in the form of muscle lipids, that are needed for successful spawning. Using species biological data, toxicological and ecotoxicological information, hypotheses are given to assess the contribution of pollution from freshwater sources to the recorded decline in the American and European eels fisheries since the 1980s. This paper first describes the lipid storage problems and the relative migratory capacities. Then several studies on the accumulation of xenobiotics in various anatomical compartments, on the biological half-lives of these compounds, and on their sublethal toxicity, are reviewed. During migration, lipid mobilization returns persistent lipophilic pollutants back into circulation, these being concentrated particularly in gonads at the crucial time of gametogenesis. Extrapolation of toxicological analysis (individual physiology) to the population level (spawning success) suggests that the quality of future spawners leaving freshwaters is one of the prime factors for the conservation of this threatened species.