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The levels of three hexabromocyclododecane (HBCD) isomers and ΣHBCDs in 54 wild and 11 farmed seafood samples collected from four regions of Japan were determined by LC/MS/MS. For the fish classified as Anguilliformes, Perciformes, Clupeiformes and farmed Salmoniformes, the medians (ranges) of ΣHBCDs are 2.09 (0.05–36.9), 0.75 (ND–26.2), 0.12 (0.09–77.3) and 1.29 (1.09–1.34) ng
g
−1
ww, respectively. However, HBCDs were not detected in samples classified as Crustacea, Mollusca, Pleuronectiformes and Scorpaeniformes, or if detected, the levels were very low. The rank correlation between ΣHBCDs (or α-HBCD) and fat content could not be found except for the Japanese sea bass of the Tohoku region. In HBCD isomer profiles, for fish samples above 20
ng
g
−1
ww, the trend was found that γ-HBCD was predominant, which suggests the influence of discharge from a nearby industrial plant. In the other wild fish and the farmed fish samples, on the other hand, α-HBCD was mostly predominant, which suggests biomagnification via the food chain. Additionally, to assess the risk to human health, based on the determined HBCD median concentrations for Anguilliformes, farmed Salmoniformes and Perciformes, the daily intake of HBCDs from fish by an average Japanese adult was tentatively calculated to be 3.7, 2.3 and 1.3
ng (kg body weight)
−1
d
−1, respectively.