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Protozoan parasites such as Trypanosoma cruzi, Leishmania spp, and Plasmodium spp have ancient histories of coevolution and complex interactions with their mammalian hosts. In order to survive against hostile environments created by the host's defense mechanisms highly adapted parasites have been selected, possessing biologic, metabolic and enzymatic features that allow them to survive and multiply within the mammalian host. Although these unique features may represent obstacles for parasite eradication, they may also be the key for development of chemotherapeutics with selective action. The development of new drugs with high efficacy and low toxicity against these protozoan parasites is of great need on account of the high toxicity of many of the available drugs and to the appearance of drug-resistant parasite strains. The diseases caused by these parasites are neglected in terms of investments for drug development because they are endemic in developing countries. Although a significant amount of basic research is carried out aiming to identify new anti-protozoan molecules, only few candidate drugs have entered clinical studies and even less became available to patients due to gaps in the pipeline of drug development. Since the identification of hits and lead compounds is a critical step towards progression in the drug development pipeline, the use of combined strategies may facilitate the identification of promising compounds and their mechanism of action. The present issue brings reviews focused on different approaches and strategies than can be employed for the development of chemotherapy for diseases caused by protozoan parasites. Cruz and collaborators also highlight the need for integrated partnerships and networks between scientists in academic institutions and industry for drug development against parasitic diseases, and the importance of initiatives such as the one aiming to produce transgenic parasites, e.g. Leishmania and Plasmodium, better suited for HTS platforms in order to accelerate the screening of antiparasitic drugs.