We investigated the cooking-induced changes in concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (PCBs) (dioxins) using mackerel and beef. The concentrations of dioxins (29 congeners) were determined by isomer specific analyses and were compared between uncooked and cooked samples. The cooking procedures examined in this study included grilling as a fillet, boiling as a fillet, and boiling as tsumire (small, hand-rolled balls) for mackerel and boiling as a slice, broiling as a slice, and broiling as a hamburger for beef. Three trials were carried out for each cooking method. Generally, concentrations of dioxins were reduced in every cooking trial. When nondetected congener concentrations were assumed to be half the limit of detection for mackerel, the maximum percentage reductions of total concentrations given as 2,3,7,8-tetraCDD equivalents (TEQ) were 31% in grilling as a slice, 14% in boiling as a slice, and 21% in boiling as tsumire under the conditions of this study. In contrast, for beef, the reductions were 42% in boiling as a slice, 42% in broiling as a slice, and 44% in broiling as a hamburger. These results suggest that ordinary cooking processes with heating undoubtedly reduce the dioxin content in animal products, and the reductions estimated should be considered when dioxin intake is evaluated using contamination data for individual food items.