Cathepsin S (CTSS) is a lysosomal cysteine protease of the papain family. It plays a major role in the processing of the MHC class II associated invariant chain2 . It has been implicated in the pathogenesis of several diseases such as Alzheimer’s disease and degenerative disorders associated with the cells of the mononuclear phagocytic system. Human Cathepsin S is synthesized as a pre-pro-enzyme of 331 amino acid residues consisting of a signal peptide (residues 1-16), a pro region (residues 17-114), and the mature enzyme (residues 1150-331). Cathepsin S is less abundant in tissues than Cathepsins B, L and H. The highest levels have been found in lymph nodes, spleen, macrophages and other phagocytic cells.