Cystatins, the inhibitors of cysteine peptidases, are expressed and released by many parasitic organisms. They are participating on regulation of biological processes, e.g., the modification of the host immune response. Our study is primarily focused on identification of genes of cystatins, characterization of molecular, biochemical and immunological properties of these molecules from four model species representing the four main groups of helmints, Monogenea are represented by Eudiplozoon nipponicum. Blood-feeding monogenean E. nipponicum parasitizing the gills of common carp (Cyprinus carpio) is widely distributed Euroasian ectoparasite from Diplozooidae family. The foregoing research has been oriented toward understanding the morphology and ecology of particular species from this taxonomic group. Currently only a little is known about the mechanisms of host-parasite interactions associated with the functional molecules produced by this parasites. Among these molecules appear also cystatins - inhibitors of cysteine peptidases. They were previously proven to play a substantial role in manipulation of the host immune response by various parasitic species and thus maximizing the parasite success. By revealing the function of cystatin of E. nipponicum we would like to complete the mosaic of present knowledge concerning the molecules from diplozoid parasites, which play a role in the host-parasite interaction and discuss the function of cystatins in the context of other multicellular parasitic organisms with different biological strategies.