Bioassay-guided fractionation of the EtOH extract of the aerial parts of Baccharis uncinella C. DC. (Asteraceae) led to identification of two cinnamic acid derivatives (caffeic and ferulic acids), two flavones (hispidulin and pectolinaringenin) and a mixture of three chlorogenic acids (3,4-, 3,5- and 4,5-O-dicaffeoylquinic acids), which displayed in vitro anti-trypanosomal activity. Pectolinaringenin, hispidulin and caffeic acid showed activity against trypomastigotes of Trypanosoma cruzi, exhibiting 50% inhibitory concentration (IC50) values of 52, 81 and 56 microg/mL, respectively, while the chlorogenic acid mixture showed an IC50 value of 61 microg/mL. The flavonoids and cinnamic acid derivatives were evaluated for cytotoxicity against NCTC cells resulting in a 50% cytotoxic concentration (CC50) ranging from 33.82 to 129.1 microg/mL while the chlorogenic acids did not display cytotoxicity (CC50 >150 microg/mL). This is the first report of anti-trypanosomal activity of compounds from B. uncinella.