The Na +/I − symporter (NIS), the plasma membrane protein that actively transports I − (stoichiometry 2Na +:1I −) in thyroid physiology and radioiodide-based thyroid cancer treatment, also transports the environmental pollutant perchlorate (stoichiometry 1Na +:1ClO 4 −), which competes with I − for transport. Until now, the mechanism by which NIS transports different anion substrates with different stoichiometries has remained unelucidated. We carried out transport measurements and analyzed these using a statistical thermodynamics–based equation and electrophysiological experiments to show that the different stoichiometry of ClO 4 − transport is due to ClO 4 − binding to a high-affinity non-transport allosteric site that prevents Na + from binding to one of its two sites. Furthermore, low concentrations of ClO 4 − inhibit I − transport not only by competition but also, critically, by changing the stoichiometry of I − transport to 1:1, which greatly reduces the driving force. The data reveal that ClO 4 − pollution in drinking water is more dangerous than previously thought.