Leishmaniasis and Chagas disease afflict the poorest countries in the world. The Brazilian flora represents a rich source for the screening of potential antiparasitic compounds. In this work, we tested the total alkaloid and ethanol extracts of nine different plants from Brazilian families which produce isoquinoline alkaloids, to determine their in vitro antiparasitic effect against L. chagasi and T. cruzi parasites. Promastigotes of L. chagasi were shown to be susceptible only to the total alkaloid extracts of A. crassiflora (EC50 value = 24.89 microg/ml), A. coriacea (EC50 value = 41.60 microg/ml), C. ovalifolia (EC50 value = 63.88 microg/ml) and G. australis (EC50 value = 37.88 microg/ml). Except for the G. australis total alkaloids, all the three extracts presented a considerable activity when tested against intracellular amastigotes. The most effective alkaloid extracts were those from A. crassiflora and C. ovalifolia, which reduced the number of infected macrophages at 25 microg/ml by 86.1% and 89.8%, respectively. Among the 18 tested extracts, 16 showed anti-Trypanosoma activity. Eight extracts (A. crassiflora, A. coriacea, C. ovalifolia, D. furfuracea, D. lanceolata, S. guianensis, X. emarginata and G. australis) were the most effective against the trypomastigotes, killing approximately 100% of the parasites at the maximal concentration of 100 microg/ml. Cytotoxicity against mammalian cells was evaluated for all extracts, but potential ones showed little or no cytotoxicity and a considerable antiparasitic effect, including D. furfuracea, D. lanceolata, G. australis, S. guianensis and X. emarginata. Plants are a rich source of natural compounds, and a powerful tool for the development of new arsenals for the therapy of protozoan diseases.