1. The regulation of energy metabolism involves food intake and energy expenditure. Mitochondrial uncoupling proteins (UCP) are implicated in energy expenditure. 2. cDNA of a homologue of UCP highly expressed in rat skeletal muscle, UCP-3, is isolated and sequenced. Rat UCP-2 cDNA is also isolated and sequenced. 3. Rat UCP-3 cDNA probe hybridized two bands, a major band at 2.5 kb and a minor band at 2.8 kb in rat tissues. The mRNA was expressed at the highest level in the skeletal muscle, and moderately in the interscapular brown adipose tissue (BAT). Only weak signals were detected in the epididymal white adipose tissue (WAT) and the heart. Rat UCP-2 cDNA probe hybridized a 1.7 kb band detected widely in the whole body, especially abundant in the lung and the spleen. In contrast to the UCP-3 gene expression, the UCP-2 gene expression was expressed at substantial levels in the WAT and only at slight levels in the skeletal muscle and BAT. 4. The UCP-3 gene expression is augmented two-fold in the gastrocnemius muscle from rats fed a high-fat diet (P < 0.05). The UCP-3 mRNA levels remained unchanged in the interscapular BAT, and epididymal WAT. The levels of the UCP-2 gene expression are augmented significantly in the epididymal WAT (1.6-fold; P < 0.05), while no significant increase is observed in the gastrocnemius muscle and interscapular BAT.