By adoption of homology searches of RNA 158 753 271 bases/223 887 transcripts the 9757 contigs (>1 kb) were assembled and particular protein molecules in E. nipponicum transcriptome data were identified, e.g. peptidases/inhibitors; 29 contigs of cysteine peptidases (e.g. cathepsin L) and 7 contigs of their inhibitors (e.g. cystatins); 12 contigs of serine peptidases (e.g. cathepsin A) and 7 contigs of their inhibitors (e.g. serpin). Employing biochemical, proteomic and molecular tools, we found that cysteine peptidase activities prevailed in soluble protein extracts and excretory/secretory (E/S) products of E. nipponicum and the major part of activity was related to cathepsin L-like. Mass spectrometry revealed several tryptic peptides in E/S products matching to two translated sequences of cathepsin L genes. The dominance of cysteine peptidases of cathepsin L type in E. nipponicum resembles the situation in, e.g., fasciolid trematodes. The cathepsin L3 was cloned and expressed in both bacterial and yeasts expression systems. The recombinant enzyme was purified on Ni-NTA agarose column and the experiments focused on its molecular/biochemical properties were started.