A 1.6-kilobase full-length cDNA of a novel human cysteine protease has been isolated and sequenced. The nucleotide sequence encodes a polypeptide of 329 amino acids composed of a 15-residue N-terminal signal peptide, a 99-residue propeptide, and a mature protein of 215 amino acids. The deduced amino acid sequence contains two potential N-glycosylation sites, one located in the proregion and one in the mature enzyme. Comparison of the amino acid sequence of cathepsin O2 with that of known human lysosomal cysteine proteases revealed a substantial degree of similarity to cathepsins L and S. Northern blot analysis indicates predominant levels of expression in osteoclastomas and ovary and therefore the enzyme was named cathepsin O2. The extremely high expression levels of human cathepsin O2 in osteoclastomas suggest a major role of this novel enzyme in bone remodelling and bone related diseases.