This study was to investigate removal efficiencies and profiles of 14 polybrominated diphenyl ether (PBDE) congeners by two different types of sewage treatment work (STW) in Hong Kong: Stonecutters Island STW (SCISTW) which uses chemically enhanced primary treatment (CEPT) process and Sha Tin STW (STSTW) which adopts biological treatment. The results indicated that both SCISTW and STSTW had a high total removal efficiency for BDE-47, BDE-99 BDE-209 and total PBDEs (SCISTW: 71.6 ± 15.8, 84.7 ± 12.3, 96.0 ± 2.62 and 87.4 ± 8.02%, respectively; STSTW: 74.8 ± 9.5, 90.7 ± 9.14, 96.2 ± 2.41 and 89.3 ± 2.62%, respectively) and PBDEs were chiefly removed by sorption. However, the profile of PBDEs demonstrated that the relative proportions of BDE-28 and BDE-47 in total PBDEs markedly increased, while that of BDE-209 decreased in the effluent samples of the two sewage treatment works, especially in STSTW. The percentage of BDE-209 in total PBDEs in effluent (49.3%) of SCISTW was 21.2% lower than that in influent (70.5%), and the percentage of BDE-209 in total PBDEs in effluent (13.8%) of STSTW was 34.1% reduced from influent (47.9%). Despite overall removal, the percentage of BDE-47 in total PBDEs in effluent (17.6%) of SCISTW was 6.85% higher than that in influent (10.7%), and the percentage of BDE-47 in total PBDEs in effluent (33.5%) of STSTW was 18.1% increased from influent (16.8%). The increase in proportion of BDE-47 in the effluent might raise environmental and public health concerns. Our study is a first attempt in reporting the PBDE congener profiles in different phases of sewage treatment.