Utilization of fatty acids for energy varies among mammalian tissues and during development due to changes in expression of enzymes of mitochondrial beta oxidation. To discern whether two related nuclear genes are expressed similarly, the tissue distribution and developmental profile of the rat long- and medium-chain acyl-CoA dehydrogenase (LCAD and MCAD) mRNAs were compared. A 1451 base full-length LCAD cDNA from neonatal rat aorta was used to study mRNA accumulation in adult and fetal rat tissues. LCAD and MCAD mRNAs were expressed in aorta, heart, and brown fat at levels 8-40 fold greater than in liver, kidney, and duodenum. Brain, placenta, ovary, testes, and skeletal muscle showed the least mRNA. Western blots of adult tissues with anti-rat LCAD antiserum showed corresponding amounts of LCAD protein subunits. LCAD mRNA was detectable in heart, liver, kidney, and brain of fetal rats and increased with age. LCAD and MCAD mRNAs were present in brown fat in 2-10 fold greater amounts compared to other tissues from the newborn period to the end of the weaning period. The high level of expression of LCAD and MCAD mRNA in aorta, heart, and brown fat likely reflects the high energy requirements of those tissues. Differential expression of LCAD and MCAD mRNAs reflects not only inherent gene prescribed programs, but also external influences such as hormones and diet.