Cysteine peptidases have potent activities in the pathogenesis of various parasitic infections. Two cDNA clones encoding cysteine peptidases were isolated from Echinococcus multilocularis metacestode (EmCLP1 and EmCLP2). EmCLP1 and EmCLP2 shared high similarity to the cathepsin L-like peptidases. Immunoblot analyses demonstrated that native EmCLP1 and EmCLP2 were present in excretory/secretory products and extracts of E. multilocularis metacestodes. By immunohistochemistry, native EmCLP1 and EmCLP2 were shown to localize to the germinal layer, the brood capsule and the protoscolex. Recombinant EmCLP1 and EmCLP2 expressed in Saccharomyces cerevisiae exhibited substrate specificity against synthetic peptidyl substrates, Z-Leu-Arg-MCA and Z-Phe-Arg-MCA. Furthermore, recombinant enzymes degraded IgG, albumin, type I and IV collagens, and fibronectin, which suggested those key roles in parasite-host interactions. This is the first report of cysteine peptidases from E. multilocularis, and would contribute to control E. multilocularis infections by chemotherapeutic drugs and/or immunoprophylaxis.