Until the recent spread of public-private partnerships, pharmaceutical firms had avoided research and development into neglected tropical diseases (NTDs). Because these are diseases that affect the poorest populations in developing regions, research and development initiatives have for the most part depended on the resources and expertise drawn from academia, international organizations, and intermittent state interventions in disease-endemic countries. Over the last few decades, however, public-private product development partnerships (PDPs) have been introducing new collaborative agreements in which the existing resources and expertise combine with the those traditionally withheld by the pharmaceutical industry and global health NGOs. This paper explores recent transformations in the representation of NTDs by examining the shifting logic and spaces of knowledge production which the advent of PDPs has enabled. An analysis of two case studies focused on Chagas disease-related initiatives addresses recurring preoccupations in Science, Technology and Society studies as well as in critical analyses of PDPs: that is, the back-and-forth movement of the disease from being an object of scientific inquiry to a public health concern, and the legitimacy risks and material asymmetries entailed in global health PDPs. Both cases show that it is major global health stakeholders and experts in non-endemic countries, rather than transnational pharmaceutical firms, that exert the greatest influence upon these changing representations: PDPs attempt to expand the preexisting biomedical focus on NTDs by means of incorporating “real world” drug development preoccupations (which I term epistemic shifts), but they also combine their stated global humanitarian aim with security concerns about the diseases spreading to non-endemic, industrialized countries (which I term geographical shifts).