Cysteine proteases have been identified as promising targets for the development of antiparasitic chemotherapy. An attractive aspect of these enzymes is their widespread importance in both protozoan and helminth parasites of domestic animals and humans. Concerns about the ability to selectively inhibit parasite proteases without affecting host homologues have been addressed in recent studies of Trypanosoma cruzi and Plasmodium falciparum. Significant data on half-life, metabolism, pharmacokinetics and safety have been accumulated. Differential uptake of proteases by parasitic organisms versus host cells, and relatively less redundancy in parasite protease gene families, may be two factors which contribute to the successful treatment of animal models of infection.