In our search for new antiprotozoal chemotherapy, we collected a selection of 26 plants used in Mexican traditional medicine for the treatment of gastrointestinal disorders. Methanolic extracts of these species were screened for their antiprotozoal activity against Entamoeba histolytica and Giardia lamblia trophozoites using in vitro tests. Among the tested extracts, the derivates of following species showed selectivity and significant antiprotozoal activity: Chiranthodendron pentadactylon, Annona cherimola and Punica granatum were the most active on Entamoeba histolytica with IC50 < 30 microg/ml. Dorstenia contrajerva, Senna villosa and Ruta chalepensis were the most active toward Giardia lamblia with IC50 < 38 microg/ml. The potency of Chiranthodendron pentadactylon (IC50 2.5 microg/ml) on Entamoeba histolytica was close that of to emetine, but far less than metronidazole, drugs used as control. The results of the antiprotozoal screening support the popular uses of the studied species for the treatment of diarrhoea and dysentery in Mexican traditional medicine.