The effort to understand the mechanism of uncoupling by UCP has devolved into two models - the fatty acid protonophore model and the proton buffering model. Evidence for each hypothesis is summarized and evaluated. We also evaluate the obligatory requirement for fatty acids in UCP1-mediated uncoupling and the question of fatty acid affinity for UCP1. The structural bases of UCP transport function and nucleotide inhibition are discussed in light of recent mutagenesis studies and in relationship to the sequences of newly discovered UCPs.