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Mercury (Hg), cadmium (Cd) and zinc (Zn) concentration were analysed in muscular and liver tissues of two cetacean species, franciscana Pontoporia blainvillei and boto-cinza Sotalia guianensis, in order to compare their contamination levels in northern Rio de Janeiro State, south-eastern Brazil. The cutlassfish, Trichiurus lepturus, which is the preferential prey of the boto-cinza, have also been analysed. Liver tissue always presented higher concentrations when compared with muscle samples for all the studied metals. The boto-cinza showed higher concentrations for all metals in both tissues than in the franciscana, and the only exception was Cd. This result is probably related to the difference in size prey preference of each cetacean. Mercury was the only element that presented significant positive correlations with body length and age in both cetacean species. The cutlassfish showed rising Hg concentrations with weight and total length, suggesting a possible mercury pathway for marine mammals' contamination.