Hookworms possess potent immunoregulatory properties. Support for this notion comes from immune-epidemiological observations in hookworm-endemic countries, clinical trials involving experimental infection of volunteers with hookworms, and studies with animal models of inflammatory diseases. As proof-of-concept for the therapeutic benefits of helminth therapy, we have completed a small open label clinical trial using trace gluten consumption coupled with hookworm as an immunoregulatory agent to treat coeliac disease. Beyond our expectations, the treatment resulted in improved gluten tolerance, improved coeliac disease activity measurements and increased regulatory T cell (Treg) numbers in the intestinal epithelium. Despite the promising efficacy of live helminth therapy, the approach has major drawbacks for wide-spread implementation. Central to the hookworm’s ability to modulate inflammation is the excretory/secretory (ES) component, the parasite’s public face of the host-pathogen interactome. We have characterised the hookworm secretome using genomics and targeted proteomics of the ES proteins. At least one family of abundant ES proteins with therapeutic properties in mouse models of asthma and colitis has been identified, and one of these proteins (AIP-2) is undergoing further development as a novel biologic for treating IBD. Like most other pathogens, approximately half of the hookworm’s secreted proteins have no known function, precluding bioinformatics-based predictions of a biological role. To address the roles of these novel parasite proteins, we are producing a hookworm recombinant secretome using a cell-free Leishmania rapid in vitro translation system. Unpurified recombinant lysates are screened for (1) anti-inflammatory properties in a mouse model of chemical colitis, and (2) novel host-parasite protein-protein interactions by probing human proteome microarrays. Using these approaches we have identified new anti-inflammatory ES proteins as well as binding partners for hookworm proteins of unknown function. This method of high-throughput protein production coupled to both rapid anti-inflammatory in vivo screening and host-parasite protein-protein interactions is amenable to the secretomes of other human pathogens, and shows great promise for assigning functions to important pathogen proteins and the discovery of new therapeutics from immunoregulatory pathogens.