Helminth pathogens prepare a Th2 type immunological environment in their hosts to ensure their longevity. They achieve this by secreting molecules that not only actively drive type 2 responses but also suppress type 1 responses. Here, we show that the major cysteine proteases secreted from the helminth pathogens Fasciola hepatica (FheCL1) and Schistosoma mansoni (SmCB1) protect mice from the lethal effects of lipopolysaccharide by preventing the release of inflammatory mediators, nitric oxide, interleukin-6, tumor necrosis factor ␣, and interleukin-12, from macrophages. The proteases specifically block the MyD88-independent TRIF-dependent signaling pathway of Toll-like receptor (TLR)4 and TLR3. Microscopical and flow cytometric studies, however, show that alteration of macrophage function by cysteine protease is not mediated by cleavage of components of the TLR4 complex on the cell surface but occurs by degradation of TLR3 within the endosome. This is the first study to describe a parasite molecule that degrades this receptor and pinpoints a novel mechanism by which helminth parasites modulate the innate immune responses of their hosts to suppress the development of Th1 responses.To establish successful chronic infections, helminth parasites induce potent Th2 immune responses, which can only occur when Th1 cytokines are suppressed (1). To create this anti-inflammatory environment helminths secrete molecules that prevent dendritic cells and macrophages responding to Toll-like receptor (TLR) 2 Th1-stimulating ligands such as LPS and CpG (2-5). It has been proposed that helminth-secreted molecules themselves signal through TLRs, activating a different pattern of kinases compared with LPS, resulting in the extracellular signal-regulated kinase dependent inhibition of interleukin (IL)-12 production (reviewed in Ref. 6). The molecular nature of these Th1-suppressing components, however, remains largely unknown.Enzyme activity ascribable to the papain family of cysteine proteases (clan CA, family C1), such as cathepsin L and B, has been identified as a major component of the secretions of almost all helminth parasites of humans, livestock, and companion animals (7,8). These proteases are pivotal to the parasitic lifestyle by mediating fundamental processes such as host invasion, acquisition of nutrients, and the migration through host tissues (reviewed in Ref. 9). They can also have a systemic effect on the immune responses of their hosts by cleaving immunoglobulins and preventing antibody-mediated immune effector function, which protects the parasites from immune elimination (10, 11). We have shown that the predominant secreted product of the human and animal helminth pathogen Fasciola hepatica, a cathepsin L1 cysteine protease (FheCL1), suppressed the onset of protective Th1 immune responses in mice to infections with the respiratory microbe Bordetella pertussis, making them more susceptible to disease. In addition, injection of the cysteine protease immediately prior to immunization of mice with a B. pertussis whole...