In addition to kaempferol and quercetin already found in the roots from Cuphea pinetorum, bioassay-guided fractionation of the crude extract of the aerial part of this species gave four flavonoid glycosides, quercetin-3-O-alpha-rhamnopyranoside, luteolin-7-O-beta-D-glucopyranoside, apigenin-7-O-alpha-L-rhamnopyranoside and apigenin-7-O-beta-D-glucopyranoside, as well as squalen and beta-sitosterol. In vitro antiamoebic and antigiardial activities of isolated compounds indicated that kaempferol is the principal antiprotozoal agent in C. pinetorum. Based on finding this antiprotozoal inhibitor, flavonoids were studied in order to elucidate structure-activity relationships. These data suggest that kaempferol may play an important role in antidiarrhoeal activity of C. pinetorum