Four new Co(II)-coordination polymers have been prepared from treatments of a Coll source with bis[2-(1H-imidazol-1-yl)ethyl]ether (bie) or 1,5-bis(1H-imidazol-1-yl)pentane (bipen), which are bis-imidazole-type ligands with hydrophobic polymethylene units. Structural characterizations have shown that their compounds create hydrophobic cavities for anions in their cationic 3D coordination frameworks. The self-assembled construction of the frameworks in aqueous solutions containing various inorganic anions trapped perchlorate ion selectively in the cavities. Because the product is insoluble in water, perchlorate ion was selectively removed from the aqueous solutions.