This study is to elucidate the specific accumulation of 20 trace elements in tissues/organs of great cormorants from two different colonies (Lake Biwa and Mie) in Japan. In the body distribution of trace elements, some elements revealed tissue-specific accumulation such as most of the burden of Mo, Ag and Cd in liver, Tl and Cd in kidney, Cu, Rb and Cs in muscle, and V, Sr and Ba in bone. Gender-related variation was not observed in both populations for most of the trace elements, except for higher hepatic Sr in males from Lake Biwa. Hepatic V, muscular Hg and Tl, and Cd in liver, kidney and muscle increased with growth. Comparison of trace element levels in tissues between the two colonies showed that Cr, Rb, Sr, Cd, Cs, Ba and Tl levels were higher in Lake Biwa than in Mie, whereas Zn, Co and Hg in Mie samples were greater than Lake Biwa. Variations of elemental levels in stomach contents also showed similar patterns, thus, showing that dietary sources tended to be the main factor for these regional variations. Toxic Hg and Cd concentrations in the liver of cormorants from the two colonies were lower than those from other areas, implying relatively low exposure to these metals in the present study sites. Concentrations of V, Co, Ag, Cd, Cs, Hg, Tl, Pb and Bi in liver remained more or less at the same level between 1993 and 2003, while hepatic Cr, Mn, Cu, Zn, Se, Rb, Sr and Ba showed apparent decrease, which might be related to the biological factors.