Nonesterified long-chain fatty acids have long been known as uncouplers of oxidative phosphorylation. They are efficient protonophores in the inner mitochondrial membrane but not so in artificial phospholipid membranes. In the un-ionized form, they undergo a rapid spontaneous transbilayer movement (flip-flop). However, the transbilayer passage of the dissociated (anionic) form is hindered by the negatively charged hydrophilic carboxylic group. In the inner mitochondrial membrane, the transfer of fatty acid anions is mediated by the adenine nucleotide translocase, the dicarboxylate carrier, and the glutamate/aspartate carrier. As a result, the passage of protons and electric charges is a concerted effect of the spontaneous flip-flop of the undissociated (protonated) form in one direction and carrier-facilitated transfer of the ionized (deprotonated) form in the other direction. In addition, fatty acids also promote opening of the mitochondrial permeability transition pore, presumably due to their interaction with one of its constituents, the adenine nucleotide translocase, thus forming an additional route for dissipation of the proton gradient. Structural prerequisites for these proton-conducting mechanisms are (1) a weakly ionized carboxylic group and (2) a hydrocarbon chain of appropriate length without substituents limiting its mobility and hydrophobicity.