In this study, we analyzed the concentrations of mercury and dioxins in tuna with various fat contents (akami; the leaner meat, Chutoro; the belly area of the tuna along the side of the fish between the akami and the otoro. Otoro; the fattiest portion of the tuna) in wild and farmed bluefin tuna and farmed southern bluefin tuna. In the three kinds of tuna, average dioxins concentrations in Akami, chutoro and otoro were 1.7, 4.7 and 9.6 pg TEQ/g, respectively. The dioxins concentration in all three regions of tuna was in direct proportion to the fat content. In the farmed bluefin tuna, the dioxins concentration was almost the same as that of the wild tuna, but differed from that of the farmed southern bluefin tuna. Average total mercury concentration based on wet weight in akami was 0.42 µg/g, being higher than the values of 0.36 µg/g of chutoro and 0.31 µg/g of otoro, and in inverse proportion to the fat content. In all three regions, the total mercury concentration of the wild bluefin tuna was equal to that of the farmed tuna. The total mercury concentration in the latter was two to three times higher than that of the farmed southern bluefin tuna. If the Japanese intake is one fin of tuna (80 g) a day, the daily intake levels of dioxins and methyl mercury can be estimated as 0.48-37 pg TEQ/kg bw and 0.21-0.90 µg/kg bw, respectively.