Little is known about the distribution of polybrominated diphenyl ethers (PBDE) -also known as flame retardants- in major ocean compartments, with no reports yet for the large deep-water masses of the Arctic Ocean. Here, PBDE concentrations, congener patterns and inventories are presented for the different water masses of the pan-Arctic shelf seas and the interior basin. Seawater samples were collected onboard three cross-basin oceanographic campaigns in 2001, 2005, and 2008 following strict trace-clean protocols. ∑14PBDE concentrations in the Polar Mixed Layer (PML; a surface water mass) range from 0.3 to 11.2 pg·L(-1), with higher concentrations in the pan-Arctic shelf seas and lower levels in the interior basin. BDE-209 is the dominant congener in most of the pan-Arctic areas except for the ones close to North America, where penta-BDE and tetra-BDE congeners predominate. In deep-water masses, ∑14PBDE concentrations are up to 1 order of magnitude higher than in the PML. Whereas BDE-209 decreases with depth, the less-brominated congeners, particularly BDE-47 and BDE-99, increase down through the water column. Likewise, concentrations of BDE-71 -a congener not present in any PBDE commercial mixture- increase with depth, which potentially is the result of debromination of BDE-209. The inventories in the three water masses of the Central Arctic Basin (PML, intermediate Atlantic Water Layer, and the Arctic Deep Water Layer) are 158 ± 77 kg, 6320 ± 235 kg and 30800 ± 3100 kg, respectively. The total load of PBDEs in the entire Arctic Ocean shows that only a minor fraction of PBDEs emissions are transported to the Arctic Ocean. These findings represent the first PBDE data in the deep-water compartments of an ocean.