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The analysis of brominated flame retardants, such as polybrominated diphenyl ethers (PBDEs), has received increased interest because of their toxicity and ubiquity. According to European Union Directive 2008/105/EC, the development of highly sensitive and selective methods capable of determining PBDEs at low concentration levels (<0.5 ng/L) is necessary. In this work, an SPE method was developed for the analysis of the six PBDEs (BDE-28, BDE-47, BDE-99, BDE-100, BDE-153, BDE-154) specified by the aforementioned directive in surface waters. The analyses were performed by GC coupled to magnetic sector high-resolution MS. The conditions were also optimized to detect the target compounds in water samples at concentrations below the environmental quality standards established by European legislation. The validated method provided adequate linearity (determination coefficient, R(2) ≥ 0.9960), recovery (101-120%, except for BDE-47 at 5 ng/L, 127%), and precision values (RSD < 20%) at two fortification levels (0.2 and 5 ng/L). The method showed LODs and LOQs ranging from 0.02 to 0.05 and from 0.05 to 0.1 ng/L, respectively. The method was applied in surface water samples, allowing the determination of these compounds at the limits established by current legislation.