Gas chromatography coupled to low-resolution mass spectrometry with electron capture negative ionization as detection mode (GC-LRMS (ECNI)) has been compared to gas chromatography coupled to high-resolution mass spectrometry using electron ionization as detection mode (GC-HRMS (EI)) for determination of polybrominated diphenyl ethers (PBDEs) in biological samples. Extracts of 5.0 g plasma, serum and milk samples were analyzed using both methods. The GC-LRMS (ECNI) and GC-HRMS (EI) systems were found to be equally well suited for determination of PBDEs in the biological samples, as well as in standard solutions, with respect to response, detection limits and repeatability at the pg-level. The estimated limits of detection (LOD) in milk extracts ranged from 0.3-0.6 pg PBDE/g milk and 0.4-0.7 pg PBDE/g milk, for the GC-LRMS (ECNI) and GC-HRMS (EI) systems, respectively. The method repeatability including sample preparation was in the range 4.7-8.4% and 0.6-10% relative standard deviation (RSD) for the GC-LRMS (ECNI) and GC-HRMS (EI) systems, respectively.