In preparation for gene manipulative experiments in mice we have isolated genomic clones covering the entire murine cathepsin K gene (Ctsk). Sequence analysis revealed that the gene spans 10.1 kb and contains eight exons and seven introns. The sizes of the coding exons 2-7 as well as the pattern of intron sizes are conserved between the human and mouse cathepsin K genes. Genomic organization of the mouse cathepsin K gene also closely resembles those of cathepsins S and L. More than 26% of the Ctsk sequence consists of different repetitive elements. Detailed sequence analysis of 1.7 kb of Ctsk promoter revealed several putative binding sites for transcription factors and two stretches of 280-320 bp which were > 70% homologous with the human cathepsin K promoter. Analysis of genomic clones extending further upstream of the Ctsk gene identified the 3' end of the gene coding for arylhydrocarbon-receptor nuclear translocator (Arnt). This places Ctsk approximately 4.5 kb downstream of Arnt on mouse chromosome 3 at locus 47.9.