The chromatographic and mass spectrometric (MS) behaviors of 49 polybrominated diphenylether (PBDE) homologues toward various techniques is investigated. Special attention is paid to chromatographic separation, ionization processes, and signal acquisition modes. Different liquid chromatographic (LC) separation systems and gas chromatographic (GC) temperature program parameters are studied. For LC-MS experiments, the ionization efficiencies of electrospray, atmospheric pressure chemical ionization, and atmospheric pressure photoionization (APPI) are evaluated. For GC-MS experiments, negative chemical ionization with ammonia as reagent gas as well as negative and positive electron impact (EI) ionization are studied. Thus, fragmentation pathways of PBDEs are investigated, with the main objective being to determine the sensitivity/specificity balance of each tested technique with respect to their potential respective application (parent compound focusing, metabolite identification, and screening of analogue compounds). Finally, performances of the different tested techniques are compared and evaluated in terms of detection limits on standard solutions for each homologue group. In terms of ionization, EI remains the best compromise between sensitivity and specificity with possible complementary applications in MS-MS and high-resolution MS. Nevertheless, APPI appears to be a promising alternative.