During the development of a method to determine polybrominated diphenyl ethers (PBDEs) using GC/MS-MS equipped with a programmed temperature vaporizer (PTV) injector, a dramatic decrease in sensitivity to decabromodiphenyl ether (BDE-209) occurred and lack of sensitivity and repeatability was observed. An alternative method using GC/ECD equipped with an on-column injector was evaluated for this congener optimizing pre-column and column length. A coated retention gap (50 cm of length, 0.53 mm I.D., 0.15 microm d(f)) connected to a short capillary column (7 m of length, 0.32 mm I.D., 0.25 microm d(f)) showed the better sensitivity and repeatability. Finally, a double system based on the programmed temperature vaporizer injector/MS detector (for tri- to hepta-BDEs) and on-column injector/electron-capture detector (for BDE-209) was evaluated using two candidate certified materials (fish muscle tissue and river sediment).