In comparison to the huge number of peptidic and peptidomimetic inhibitors of cysteine proteases which have been developed during the last twenty years the number of non-peptidic compounds with cysteine protease inhibiting properties is restricted to a few substance classes. In contrast to peptidic and peptidomimetic inhibitors the non-peptidic lead structures have mainly been discovered by computational or enzymatic industrial screenings and not by a rational approach. But, the growing number of resolved X-ray structures of the target enzymes as well as molecular modeling methods have supported the further development of potent inhibitors beginning from these lead structures. In this review we will focus on new non-peptidic cysteine protease inhibitors which have been developed during the last years. Discovery, structure-activity-relationship and inhibition mechanisms will be discussed.