Japanese cranes (Grus japonensis) of eastern Hokkaido, Japan, and migrants between the Amur River basin and the eastern China-Korea Peninsula, live around fresh and brackish wetlands. Only a few thousand cranes are confirmed to exist in the world, so they are under threat of extinction. To understand the adverse effects of metal accumulation, we measured concentrations of three heavy metals in the liver, kidney, and muscle of 93 Japanese cranes from Hokkaido. The cranes were classified into six categories according to their sex and three life stages. Cadmium and mercury (Hg: total mercury) showed age-dependent but not sex-dependent accumulation in the liver and kidney. Twenty cranes showed 30 microg/g or higher levels of Hg in dry tissue and five adult cranes had more than 100 microg/g in their livers or kidneys. Cadmium concentrations were generally lower in all samples. Two adult cranes showed extremely high lead levels of more than 30 microg/g in their livers, suggesting lead poisoning. These results have highlighted the widespread and high levels of Hg pollution in Japanese cranes in Hokkaido, Japan.