Synthetic and natural naphthofuranquinones were tested in vitro against three Trypanosoma cruzi strains with different drug susceptibility to nifurtimox and benznidazole/n vivo. Four compounds exhibited high trypanoeidal activity. No difference in drug susceptibility was found among the strains, therefore showing no correlation between the in vitro activity of those compounds and the in vivo results with the classic drugs.