cDNA encoding the precursor of rat very-long-chain acyl-CoA dehydrogenase (VLCAD) was cloned and sequenced. The longest cDNA insert had 2117 bases. This cDNA encodes the entire protein of 655 amino acids, including a 40-amino acid leader peptide and a 615-amino acid mature polypeptide. The identity of the VLCAD clone was confirmed by matching the amino acid sequence predicted from the cDNA to the NH2 terminus and seven internal proteolytic peptide sequences from purified rat liver VLCAD. The calculated molecular masses of the precursor protein, the mature protein, and the leader peptide are 70,961, 66,508, and 4,470 daltons, respectively. At the amino acid level, the significant homology to the other acyl-CoA dehydrogenases was found at the range from the 94th to the 473rd amino acid residue of the amino-terminal side. The catalytic residue and the residue lying near the dimethylbenzene side (si-side) of the flavin ring were speculated to be Glu-462 and Trp-249, respectively. The VLCAD cDNA was expressed in four kinds of hepatoma cells using a vaccinia virus expression system and was shown to encode the catalytically active enzyme. The cDNA expression in both rat hepatoma H4IIEC3 and McA-RH7777 enhanced about 3-fold mitochondrial beta-oxidation activity of long-chain fatty acids such as palmitic acid and stearic acid; hence, VLCAD is probably a rate-limiting enzyme in the long-chain fatty acid beta-oxidation system in these cell lines.