Cysteine proteases play numerous indispensable roles in the biology of parasitic organisms. Aside from previously known general catabolic functions and protein processing, cysteine proteases may be key to parasite immunoevasion, excystment/encystment, exsheathing and cell and tissue invasion. Parasite cysteine proteases are unusually immunogenic and have been exploited as serodiagnostic markers and vaccine targets. Although host homologues exist, parasite cysteine proteases have distinct structural and biochemical properties including, pH optima and stability, the alteration in peptide loops or domain extensions, diverse substrate specificity and cellular location. The disparate nature of parasite cysteine protease compared to the host orthologous proteins has opened opportunities for chemotherapy. This review will highlight recent research on the 'papain-like' class of cysteine proteases, the most abundant family, and the newly discovered class of asparaginyl-endopeptidases. Cysteine protease classification will be re-examined in light of the diversity uncovered within parasitic organisms.