A recent hypothesis concerning the function of uncoupling protein-3 (UCP-3) depends upon a positive relationship with mitochondrial thioesterase (MTE-1) in situations where fatty acid P-oxidation is increased. MTE-1 mRNA levels are raised in transgenic mice overexpressing UCP-3 in skeletal muscle and we sought to extend these findings by quantifying in vivo expression of endogenous MTE-1, UCP-1, UCP-2, and UCP-3 mRNA levels in white adipose tissue, interscapular brown adipose tissue, and skeletal muscle in db/db mice. In this study we show that changes in MTE-1 mRNA levels as a result of differences between db/db vs db/+ mice or following long-term treatment of db/db mice with rosiglitazone or Wy-14,643 were more closely correlated with changes in UCP-3 than either UCP-1 or UCP-2 mRNA levels in the tissues examined. The present data contribute to the argument that UCP-3 and MTE-1 are linked within the same metabolic pathway either in response to, or as regulators of, fatty acid beta -oxidation.