Amoebiasis caused by Entamoeba histolytica is associated with high morbidity and mortality becoming a major public health problem, especially in developing countries. Because of the side-effects and the resistance that pathogenic protozoa build against the antiparasitic drugs, e.g. metronidazole, much recent attention has been paid to plants used in traditional medicine around the world in order to find new antiprotozoal agents. We collected 32 Mexican medicinal plants and the methanolic extracts of these species were screened for antiprotozoal activity against E. histolytica tropohzoites using in vitro tests. Each extract was dissolved in DMSO (150 µg/mL) and a 50 µl subsample was adjusted with 950µL of E. histolytica at logarithmic phase suspension in peptone, pancreas and liver extract medium containing 10% of bovine serum. Vials were incubated for 72h. After this time, the number of dead trophozoites per milliliter was determined by using a hematocytometer and inhibition percentage was estimated. Only 15 plant extracts showed more than 50% inhibition against E. histolytica and IC50 of these extracts were determined. We are presenting the results of this biological evaluation as well as the preliminary findings of the bioactivity guided isolation of natural products from Lippia graveolens Kunth and Ruta chalepensis Pers that showed the more significant antiprotozoal activity (91.50 and 90.50% growth inhibition with an IC50 of 59.14 and 60.07µg/ml, respectively).