Parasitic diseases cause annual mortality of more than 200 thousand people. Currently many drugs are used to treat parasitic diseases; however, they are mostly expensive, toxic, with side effects and drug resistance. Medicinal plants have been shown to represent natural source of cheap drugs with low toxicity. In this review article, the most common and most effective herbal medicines on pathogenic protozoan Sarcomastigophora branches such as Trypanosoma, Leishmania, Amoeba, Trichomonas and Giardia were reviewed. The recently published papers about different drugs as well as herbal medicines as alternative for synthetic drugs were searched using scientific sites such as Medline, PubMed and Google Scholar. The used terms included: Medicinal plants, herbal medicine, protozoa, Trypanosoma, Sarcomastigophora branches, Leishmania, Amoeba, Trichomonas or Giardia.