Levels of mercury (Hg) and organochlorine compounds (OCs), such as PCBs and p,p'-DDE, as well as the stable isotope ratios of carbon (delta 13C) and nitrogen (delta 15N) were compared in Pacific bluefin, yellowfin, and albacore tuna taken from the southern, central, and northern regions of Japan according to tuna species and the region of origin. Levels of Hg and OCs as well as the delta 15N value were the highest in the bluefin tuna, reflecting their higher trophic position and longer life span. The average Hg concentrations tended to be higher in specimens taken in the southern region than in the central and northern regions for bluefin tuna and in the southern region than in the central region for yellowfin and albacore tuna, while the levels of OCs tended to be lower in the southern region except for yellowfin tuna. The spatial differences in Hg and OCs levels found in the three species may reflect geographical differences in the contamination of marine environment around Japan. Negative correlations between delta 13C and delta 15N were found in the yellowfin and albacore tuna, probably reflecting the latitudinal effect, whereas a positive correlation was found in the bluefin tuna, probably reflecting a diet shift during wide-range migration.