The uncoupling protein generates heat by catalyzing electrophoretic proton transport across the inner membrane of brown adipose tissue mitochondria. It also transports Cl- and other monovalent anions, and both proton and anion transport are inhibited by purine nucleotides. Several long-standing hypotheses bear on specific aspects of Cl- transport, H+ transport, and nucleotide gating mechanisms in uncoupling protein. We reevaluated these hypotheses in mitochondria and liposomes reconstituted with purified uncoupling protein; GDP inhibition is strictly noncompetitive with Cl- and unaffected by either transmembrane electrical potential or fatty acids. The Km and Vmax values for Cl- are independent of pH, arguing against a common binding site for Cl- and OH- ions. Cl- transport was inhibited by fatty acids and stimulated by fatty acid removal, refuting the consensus hypothesis that there is no interaction between fatty acids and anion transport through uncoupling protein. These results support a mechanism in which the transport pathway for anions is identical with the fatty acid binding site and distinct from the nucleotide binding site.