The extent of bioaccumulation of hexabromocyclododecane (HBCD) isomers (alpha, beta, and gamma) was determined in the Lake Ontario pelagic food web using liquid chromatography tandem mass spectrometry (LC/MS/MS). Concentrations of the alpha-isomer were consistently higher than that of the gamma-isomer. The beta-isomer was below method detection limits in all samples. Whole body concentrations (ng/g, wet wt) of alpha- and gamma-HBCD were highest in the top predator lake trout samples ranging from 0.4 to 3.8 ng/g for the alpha-isomer and 0.1 to 0.8 ng/g for the gamma-isomer. For the prey fish species, the trends in alpha- and gamma-HBCD levels were slimy sculpin > smelt > alewife. Mean concentrations of total (sigma) HBCD (sum of alpha- and gamma-isomers) in the macrozooplankter Mysis relicta (0.14 +/- 0.02 ng/g wet wt) and in the benthic invertebrate Diporeia hoyi (0.16 +/- 0.02 ng/g, wet wt) were similar and approximately twice as high as in plankton (0.06 +/- 0.02 ng/g, wet wt). A strong positive linear relationship was found between sigmaHBCD concentrations (wet wt) and trophic level based on delta15N suggesting that HBCD biomagnifies in the Lake Ontario food web. The trophic magnification factor (TMF = 6.3) derived from the slope of the sigmaHBCD - trophic level relationship was slightly higher than TMFs for p,p'-DDE (6.1) and sigmaPCBs (5.7) found previously. Biomagnification factors (BMF, calculated as the ratio of lipid corrected concentration in predator/lipid corrected concentration in prey) were variable between feeding relationships and ranged from 0.4 to 10.8 for the alpha-isomer and from 0.2 to 10 for gamma-isomers.