Proteases, also known as proteolytic enzymes, are enzymes that catalyze the breakdown of proteins by hydrolysis of peptide bonds. By cleaving proteins, proteases are involved in the control of a large number of key physiological processes such as cell-cycle progression, cell proliferation and cell death, DNA replication, tissue remodeling, haemostasis (coagulation), wound healing and the immune response. So far, inappropriate proteolysis has been found to have a major role in cancer as well as cardiovascular, inflammatory, neurodegenerative, bacterial, viral and parasitic diseases. Because excessive proteolysis can be prevented by blocking the appropriate proteases, this area is widely explored by pharmaceutical companies. Their mechanism of action classifies the large family of proteases as either serine, cysteine or threonine proteases (amino-terminal nucleophile hydrolases), or as aspartic, metallo and glutamic proteases (with glutamic proteases being the only subtype not found in mammals so far). Interestingly, the serine and cysteine proteases act directly as nucleophiles to attack the substrate (by generating covalent acyl enzyme intermediates). On the other hand, the aspartyl and zinc proteases activate water molecules as the direct attacking species on the peptide bond. Proteases of the different classes can be further grouped into families on the basis of amino acid sequence comparison, and families can be assembled into clans based on similarities in their three-dimensional structures.A wide variety of cysteine proteases (CPs) exists, that share the common feature of hydrolyzing substrates by direct nucleophilic attack of a deprotonated cysteine residue at the enzyme’s catalytic site. CPs are responsible for many biochemical processes occurring in living organisms and they have been implicated in the development and progression of several diseases that involve abnormal protein turnover. The activity of CPs is regulated among others by their specific inhibitors: cystatins. Mammalian cysteine proteinases fall into two classes: caspases and the papain superfamily comprising the papain family, calpains and bleomycin hydrolases.