The aim of this study was to evaluate antioxidant activities and cytotoxicity against human tumor cell lines of extracts from Bidens pilosa Linn. var. radiata Sch. Bip. (BP). Total phenolic and flavonoid contents of the extracts were determined by ultraviolet spectrophotometry. Furthermore, the antioxidant properties of different polarity fractions extracted from BP were evaluated using DPPH and ABTS radical scavenging test and FRAP assay. The ethyl acetate fraction (EE-BP) showed the highest antioxidant activity compared to other fractions. In addition, the anti-proliferative activities of the extracts on four human tumor cells, namely MCF-7, HepG2, MGC 803 and RKO, were investigated by MTT method. The EE-BP displayed the most remarkable anti-proliferative effect against the tumor cells, particularly RKO cell in dose- and time-dependent manner. The antioxidant activities and cytotoxicity correlated highly with the total phenolic and flavonoid contents, respectively. Furthermore, The active ingredient BP-6, namely 5,7,4'-trihydroxy-3,3'-dimethyl-flavonol, was isolated and purified with the purity above 99.00% and content of 0.15% in EE-BP detected by HPLC, which could significantly inhibit the proliferation of RKO cells with the IC(50) value of 6.66 μmol/l. In order to characterize the apoptotic RKO cells, flow cytometry and DNA fragmentation assay were performed. Apoptotic cell numbers increased in a dose-dependent manner after the treatment with different concentrations of EE-BP and BP-6 for 12 and 6 h, respectively. DNA ladders in apoptotic RKO cells could be easily visualized when exposed to 200 μg/ml of the EE-BP for 36 h. Taken together, our work indicated that BP had potentially therapeutic value against colorectal cancer.