Parasitic diseases continue to take an enormous toll on human health, particularly in developing tropical regions, where more than 200 millions people are infected with protozoan parasites belonging to the genera Plasmodium, Trypanosoma, and Leishmania, responsible for Malaria, African trypanosomiasis, and Chagas disease, and the different forms of leishmaniasis. Current antiprotozoan chemotherapeutic agents are toxic and have many decades of clinical use, with ever decreasing efficacy due to drug resistance. Therefore, there is an urgent need for the development of novel agents against protozoan parasites. In recent years, research into animal venom toxins and other molecules isolated from natural sources has intensified, focusing on the potential of these compounds to interfere with parasite physiology and/or vector biology. Venom components and their derivatives already represent more than 50 % of pharmaceuticals in clinical use, and novel drugs to treat parasitic diseases could be developed from these compounds. This chapter examines in detail the research into numerous animal venom toxins with potential to become novel clinical agents to treat protozoan-borne diseases. Also, some of these compounds are capable of inhibiting parasite establishment in the insect vector, representing good candidates to be used in the development of strategies for disease transmission control. Overall, the studies discussed here correspond to significant advances in the discovery of new antiprotozoan molecules, and highlight the potential of venoms and toxins as rich sources of relevant biologically active compounds.