Protozoan parasites are among the most prevalent pathogens worldwide. Diseases like malaria, leishmaniasis, amebiasis, and trypanosomiasis affect hundreds of millions of people. Recent advances in our understanding of the biochemistry and molecular biology of these organisms has focused attention on specific parasite molecules that are key to the parasite life cycle or the pathogenesis of the diseases they produce. One group of enzymes that plays myriad roles in these processes are the parasite-derived proteases. Different types of proteases are frequently expressed at different stages of the parasite life cycle to support parasite replication and metamorphosis. Intracellular parasites such as those that produce malaria and Chagas' disease express high levels of protease activity to efficiently degrade host proteins like hemoglobin. In other instances, such as infection with Entamoeba histolytica, the causative agent of amebiasis, proteases released by the parasite can damage host cells and tissues, contributing to host tissue damage and parasite invasion. Detailed studies of these enzymes have led to model systems for the study of parasite gene regulation, parasite metabolism, and the host-parasite interplay. In some instances, proteases appear to be promising targets for the development of new antiparasitic chemotherapy.