Understanding the metabolic pathways of polybrominated diphenyl ethers (PBDEs) is a key issue in the evaluation of their cytotoxicity after they enter the biota. In order to obtain more information concerning the metabolic pathways of PBDEs, we developed a strong electron-withdrawing pentafluorobenzoyl (PFBoyl) derivatization capillary gas chromatography/electron capture negative ionization quadrupole mass spectrometry (GC/ECNI-qMS). PFBoyl esterification greatly improves separation of the metabolites of PBDEs such as hydroxylated PBDEs (OH-PBDEs) and bromophenols (BPs) metabolites in rat liver microsomes (RLMs). On the other hand, the strong electron-withdrawing property of PFBoyl derivatized on OH-PBDEs and/or BPs makes cleavage of the ester bond on ECNI easier resulting in higher abundance of the structure-informative characteristic fragment ions at a high m/z region, which facilitate the identification of OH-PBDEs metabolites. Subsequent quantification can be performed by monitoring not only 79Br- (or 81Br-) but also their characteristic fragment ions, achieving more accurate isotope dilution quantification using GC/ECNI-qMS. These merits allow us to identify totally 12 metabolites of BDE-47, a typical example of PBDEs, in the RLMs in vitro incubation systems. In addition to the already known metabolites of BDE-47, one dihydroxylated 3,6-di-OH-BDE-47 and one dihydroxylated 3,5-di-OH-tetrabrominated dioxin were found. Moreover, the second hydroxylation took place on the same bromophenyl ring, where the first hydroxyl group was located, and was further confirmed via the identification of the dihydroxylated 2',6'-di-OH-BDE-28 of an asymmetric 2'-OH-BDE-28. This methodological development and its subsequent findings of the metabolic pathways of BDE-47 provided experimental evidence for understanding its dioxin-like behavior and endocrine disrupting risk.