The MUT locus encoding the enzyme methylmalonyl-CoA mutase is defective in mut forms of methylmalonic acidemia. This locus has been mapped to chromosome 6p12-21.1. We report cloning and characterization of this locus which comprises 13 exons spanning greater than 35 kb of the genome. The MUT locus exhibits consensus sequences for transcription, splicing, and polyadenylation. The putative promoter region was localized in a CG island 5' to exon I and was shown to direct expression of a beta-galactosidase reporter gene in cultured cells. Of interest is the observation that the first intron occurs within the 5' untranslated region, and no introns separate the mitochondrial targeting sequences and the mature apoenzyme. An informative HindIII polymorphism was localized within the coding sequence and can be assayed using the polymerase chain reaction. These studies describe the structure of the MUTlocus and provide a foundation for characterization of mutations in mut methylmalonic acidemia.