Uncoupling proteins in the inner mitochondrial membrane provide a proton “leak”, thereby uncoupling the movement of protons down the gradient and the production of ATP. There are six uncoupling proteins (UCP1-6), the largest family of nuclear-encoded mitochondrial transporters. From an evolutionary perspective they provide dramatic steps in evolution including the evolution of endothermy, as well as regulation of ROS that are fundamental to rates of aging and oxidative stress. While the function of UCP1 in nonshivering thermogensis in mammals is well established known, the functions of the other uncoupling protein homologues is less clear. We conducted this study to fill a gap in literature related to the evolution of mitochondrial uncoupling proteins. The purpose of this study was two fold. First, we surveyed the available reptile genomes and transcriptomes for the presence of the different homologues to predicted gene losses in each group. Second, we determined whether there was evidence that positive selection acted on each UCP in the amniotes—mammals and reptiles. Across 66 species, alignments made from transcriptome and genome-derived coding sequence suggest that specific UCPs are missing in several clades, and we confirmed this by examining syntenic regions among different clades and BLAST searches across newly available genomes. The cumulative analysis suggests that all six of the UCP homologues are present in mammals. The ucp1 gene was lost very early in the reptile lineage and the lost of UCP1 seems to be a repeated occurrence in multiple mammalian lineages despite its role in non-shivering thermogenesis. Further, among reptiles UCP2 was absent in birds, and UCP3 and UCP4 were absent in snakes. Branch-site tests suggest that positive selection acted on UCP2 in the branch leading to mammals and UCP4 on the branch leading to crocodiles. These results in the context of physiological comparisons can bring new insight into the functional roles of these proteins and how they vary across taxa.