To achieve the selective separation of brominated aromatic compounds, the polymer-based separation media were prepared by the fragment imprinting technique and were evaluated with high-performance liquid chromatography. In the results, the separation medium prepared with 2,6-bis-(trifluoromethyl)-benzoic acid as the template showed the selective retention abilities for 3,5- and/or 3′,5′-brominated or chlorinated bisphenol A homologues. The selective retention seems due to the shape recognition according to the alternative template molecule. Especially, the tetrabromo- or tetrachloro-bisphenol A homologues were selectively recognized by the imprinting effect.