The cathepsins are a family of lysosomal cysteine proteases that are abundant in living cells and play important roles in intracellular proteolysis. Cathepsins are necessary for cell survival, and disruption of regulation of the activity of these enzymes causes serious diseases including allergy, atherosclerosis, muscular dystrophy, Alzheimers disease and cancer. Therefore, the design of inhibitors for cathepsins is important in development of therapeutic agents. This review will focus on the features of the tertiary structure and substrate-binding specificity of cathepsins B, L, S and K, based on X-ray crystal structures of their complexes with inhibitors. To illustrate an approach to drug design, an example of structure-based design of a cathepsin B-specific inhibitor is described.