A gas chromatography–mass spectrometry (GC–MS) method was investigated for the simultaneous analysis of two types of endocrine disrupting compounds (EDCs), i.e., alkylphenol ethoxylates and brominated flame retardants (BFRs), by extraction and derivatization followed by GC–MS. Different solid phase extraction (SPE) cartridges (Cleanert PestiCarb, C18, Cleanert-SAX and Florosil), solvents (toluene, tetrahydrofuran, acetone, acetonitrile and ethyl acetate) and bases (NaHCO3, triethylamine and pyridine) were tested and the best chromatographic analysis was achieved by extraction with Strata-X (33 μm, Reverse Phase) cartridge and derivatization with heptafluorobutyric anhydride at 55 °C under Na2CO3 base in hexane. It was observed that APE together with lower substituted PBBs (PBB1, PBB10, PBB18 and PBB49), HBCD and TBBPA can be determined simultaneously under the same GC conditions. This simple and reliable analytical method was applied to determining trace amounts of these compounds from wastewater treatment plant samples. The recoveries of the target compounds from simulated water were above 60 %. The limit of detection ranged from 0.01 to 0.15 μg L−1 and the limit of quantification ranged from 0.05 to 0.66 μg L−1. There were no appreciable differences between filtered and unfiltered wastewater samples from Leeuwkil treatment plant although concentration of target analytes in filtered influent was slightly lower than the concentration of target analytes in unfiltered influent water. The concentrations of the target compounds from the wastewater treatment were determined from LOQ upwards.