Bioactivity of fractions and compounds obtained from Polygala sabulosa against Trypanosoma cruzi epimastigote, blood trypomastigote and amastigote forms were evaluated in vitro. Dichloromethane and ethyl acetate fractions showed a strong trypanocidal activity on epimastigotes (IC50< 10.4 µg/mL). Chromatographic analysis by TLC of these fractions confirmed the presence of previously described compounds (dihydrostyryl-2-pyrones, styryl-2-pyrones and 6-methoxy-7-prenyloxycoumarin). The dichloromethane fraction was fractioned by silica gel column chromatography to afford the compound α-spinasterol and the ethyl acetate fraction yielded apigenin, quercetin and a quercetin-3-O-glucoside, being the first description for the Polygala genus. 4-Methoxy-6-(11,12-methylenedioxy-14-methoxydihydrostyryl)-2-pyrone, 4-methoxy-6-(11,12-dimethoxystyryl)-2-pyrone, 6-methoxy-7-prenyloxycoumarin and quercetin-3-O-glucoside showed a weak activity against blood trypomastigotes (IC50< 1008.6 µg/mL). The prenylated coumarin was the most active compound against both epimastigote and trypomastigote forms, IC50 10.5 and 88.2 µg/mL, respectively. The hemolytic activity and cell toxicity of each active compound was also assessed. Furthermore, 4-methoxy-6-(11,12-methylenedioxy-14-methoxydihydrostyryl)-2-pyrone and 6-methoxy-7-prenyloxycoumarin reduced 4 times the T. cruzi infection rate for Vero cells at 100 and 50 µg/mL, respectively. These results show for the first time active compounds against T. cruzi in P. sabulosa.