Aldehyde oxidase was purified to homogeneity from bovine liver and primary structural information obtained by sequencing a series of cleavage peptides permitted the cloning of the corresponding cDNA. The cDNA is 4,630 base pairs long, and it consists of a 102-base pair 5'-untranslated region followed by a 4017-base pair coding region and a 511-base pair 3'-untranslated region. The open reading frame predicts a 1339-amino acid polypeptide with a calculated molecular weight of 147,441, which is consistent with the size of the aldehyde oxidase monomeric subunit. The aldehyde oxidase polypeptide contains consensus sequences for iron-sulfur centers and a molybdopterin binding site. The amino acid sequence deduced from the cDNA shows significant similarity with that of xanthine dehydrogenases from various sources. The primary structure of bovine aldehyde oxidase is remarkably similar (approximately 86%) to that of the translation product of a cDNA recently isolated by Wright et al. (Wright, R. M., Vaitaitis, G. M., Wilson, C. M., Repine, T. B., Terada, L. S., and Repine, J. E. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 10690-10694) and reported to represent human xanthine dehydrogenase. With the help of a monospecific antibody raised against the purified protein and the isolated cDNA, the tissue distribution of the bovine aldehyde oxidase protein and corresponding mRNA was determined. Aldehyde oxidase is expressed at high levels in liver, lung, and spleen, and, at a much lower level, in many other organs.