Two recently described uncoupling proteins, UCP2 and UCP3, may have important roles in determining feed conversion and/or maintenance energy requirements in livestock. Sequence was determined for the entire coding region and four of the six introns for bovine UCP3. A partial cDNA sequence was obtained for bovine UCP2. Radiation hybrid mapping was used to place UCP3 on BTA15, a chromosome previously shown to harbor a locus influencing meat tenderness. In order to place UCP3 in the existing linkage map, five single nucleotide polymorphisms (SNPs) were developed. Linkage analysis using one of five SNPs was used to place UCP3 between 53.1 and 53.5 CM. No recombination was detected between UCP3 and IDVGA10, IDVGA32, and INRA145. The sequence of PCR products from a single BAC amplified with primers specific for either UCP2 or UCP3 indicate that UCP2 and UCP3 are separated by < 200 kb.