Total mercury (T-Hg), methyl mercury (M-Hg), cadmium (Cd), selenium (Se), zinc (Zn) and copper (Cu) concentrations in the organs of melon-headed whales from a mass stranding on the Japanese coast were analyzed. The mean concentration of T-Hg in the liver (126±97 μg/wet g, n=13) was markedly higher than those in kidney (6.34±2.36 μg/wet g, n=12) and muscle (4.90±2.33 μg/wet g, n=15). In contrast, the mean concentration of M-Hg in the liver (9.08±2.24 μg/wet g) was similar to those in the kidney (3.47±0.91 μg/wet g) and muscle (3.78±1.53 μg/wet g). The mean percentage of M-Hg in the T-Hg found in the liver (13.1±10.3) was significantly lower than those in the kidney (58.3±15.0) and muscle (78.9±8.4). The molar ratio of T-Hg to Se in the liver was effectively 1.0, but those in the kidney and muscle were markedly lower. Conversely, the mean concentration of Cd was markedly higher in the kidney (24.4±7.4 μg/wet g) than in the liver (7.24±2.08 μg/wet g) and muscle (less than 0.05 μg/wet g). These results suggest that the formation of Hg–Se compounds mainly occurs in the liver after the demethylation of M-Hg, and Cd preferentially accumulates in the kidney of melon-headed whales.