Kinetoplastids, or trypanosomatids are flagellate protozoa characterized by the presence of a kinetoplast composed of a DNA network of circular molecules, localized near the basal body. Cysteine proteinases (CPs) have attracted considerable attention in pathogenic trypanosomatids due to their essential roles in parasite' growth, transformation, proliferation, migration and invasion, as well as immunomodulation of host immune system. Because CPs are essential virulence factors during all stages of the infection process, a number of new strategies to obstruct trypanosomatid biological processes have emerged; one of them is focused on using CP inhibitors (CPIs). The objective of the present review is to highlight the molecular characterization and functions of CPs in pathogenic trypanosomatids. Sufficient knowledge aided with bioinformatics analysis can lead to efficient development of diagnostic and biogenetic markers, drug targets (potent CPIs), and vaccine candidates. The role of the unusual endogenous CPI (CYS) in trypanosomatids will also be discussed.