An enzyme, O6-methylguanine-DNA methyltransferase, is present in various organisms and plays an important role in repair of DNA damaged by alkylating agents. The enzyme transfers methyl groups from O6-methylguanine and other methylated moieties of the DNA to its own molecule. As a first step to construct animal models with altered levels of the enzyme activity, we cloned cDNA and genomic DNA sequences for mouse methyltransferase and elucidated their structures. The nucleotide sequence of the cDNA revealed an open reading frame comprising 211 amino acid residues. The mol. wt of mouse O6-methylguanine-DNA methyltransferase, calculated from the predicted amino acid sequence, was 22,400, and the methyltransferase protein of this size was present when the cDNA was expressed in methyltransferase-deficient human cells. The predicted amino acid sequence of the mouse methyltransferase exhibits an intense homology with those of human and bacterial counterparts. Using the cDNA as a probe, part of the mouse gene for methyltransferase was isolated. The gene consisted of at least four exons and spanned greater than 145 kb. Sequences around the exon/intron junctions for the mouse gene are almost the same as those for the human species.