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Tropical protozoan diseases are currently a major public health problem throughout the world and are strongly linked with poverty, this combined with a lack of commercial markets for potential drugs has created a large burden on the health and economic development of low-income and middle-income countries in Africa, Asia, and the Americas. Due to the low research interest and the high increase of resistance against the existing treatments, as well as increasing inefficiency, toxicity, prolonged treatment schedules and costs, there is an urgent need for cost-effective, safe and easy-to-administer, new effective compounds with novel mechanisms of action. Several studies of crude plant extracts have already identified potential compounds to treat Chagas’ disease, Leishmaniasis, Toxoplasmosis, Giardiasis, and Malaria among other protozoan parasites. Natural compounds of medicinal plants have shown lower toxicity together with higher specificity, creating an optimistic view of new treatments for diseases. Out of 1010 new active substances approved as drugs for medical conditions by regulatory agencies during the past 25 years, 490(48.5%) were from a natural origin.