Muscle, liver and stomach contents of 64 blue sharks and 52 swordfishes, caught between September 2004 and February 2005 near the Azores (area A) and the Equator (area E), were analysed for mercury and selenium. Levels of mercury were relatively high (blue shark: 0.032-2.5microgg(-1); swordfish: 0.031-9.8microgg(-1)) and comparable to values reported in the literature. However, mercury and organic mercury concentrations in muscle and liver of specimens from E were significantly higher than those from A. A similar trend was registered in stomach contents, suggesting higher uptake of Hg in specimens from E. This difference was also observed in the relationship between concentration in muscle and size, indicating a higher accumulation rate in specimens from E. The accumulation of Se in the liver of both species showed a positive correlation with inorganic mercury concentrations, pointing to a detoxifying mechanism of organic mercury in these species through Se-Hg liasons.