A cDNA clone encoding mitochondrial vitamin D3 25-hydroxylase was isolated from a rat liver cDNA library by the use of specific antibodies to the enzyme. The isolated cDNA clone was 1.9 kbp long and contained a 1599 bp open reading frame encoding 533 amino acid residues. The deduced primary structure contained a presequence typical for mitochondrial enzymes in the N-terminal region. The N-terminal sequence of the mature enzyme was determined to be Ala-Ile-Pro-Ala-Ala, which agrees perfectly with a portion of the deduced sequence, establishing the cleavage point of the precursor.