Flavonoid compounds are normally present on nature being a common constituent of medicinal plants. These natural products have several health benefits, including activity against tropical parasites, such as Trypanosoma cruzi and Leishmania spp. Five flavonoid active against Trypanosoma cruzi and five active against Leishmania species were submitted to molecular docking with the enzymes cruzain and trypanothione reductase from Trypanosoma cruzi and N-myristoyltransferase, dihydroorotate dehydrogenase and trypanothiona reductase from Leishmania spp. Considering the binding energies and interactions between both, compounds and enzymes, the flavonoids chrysin dimethylether  and tamarixetin against T. cruzi, and luteolin and ladanein against Leishmania spp presented the best results. This study hopes to contribute to existing research on these natural products against these tropical parasites.