We compared morphologic changes in thyroid glands of great cormorants (Phalacrocorax carbo) from the Tokyo Bay and Lake Biwa areas in Japan with presence of residues of polychlorinated dibenzo-dioxins (PCDDs), polychlorinated dibenzo-furans (PCDFs), and coplanar polychlorinated biphenyls (Co-PCBs). Prominent morphologic changes in thyroid glands included increased density of small follicles and increased number of epithelial cells surrounding follicular lumens. The extent of morphologic changes in the thyroid gland was higher in cormorants captured from Tokyo Bay than in those captured from Lake Biwa. Increased thyroid change in cormorants from the Tokyo Bay area was associated with significantly higher levels of PCDFs and Co-PCBs. Thus, we suggest that morphologic changes in thyroid glands from the cormorants are associated with increased levels of dioxin contamination in Japan.