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Background/Objective: Vernonia zeylanica (L) less is an endemic plant to Sri Lanka. The present study was designed to isolate potential cytotoxic compound/s from chloroform and ethyl acetate extracts of V. zeylanica by bio-activity guided isolation and to evaluate its anti-proliferative effects in three breast cancer phenotypes (MCF -7, MDA-MB-231, SKBR-3). Methods: Combined chloroform and ethyl acetate extracts were subjected to chromatographic separations to isolate a compound (1) and the structure of the isolated compound was elucidated using 1H, 13C and mass spectroscopic techniques. Cytotoxic effects of the compound were evaluated by the sulforhodamine B (SRB) and the MTT (3- (4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assays. Effects of the compound on apoptosis were evaluated by fluorescent microscopy, caspase 3/7 activation, DNA fragmentation and real time PCR. Effects of the compound on the expression of heat shock protein complex were also evaluated by real time PCR and immunofluorescence. Results: Isolated compound was identified as a new sesquiterpene lactone (vernolactone). The compound mediated significant cytotoxic effects in SKBR-3 and MDA-MB-231 breast cancer cells, with little effect in MCF-7 and normal mammary epithelial MCF-10A cells. Morphological changes, DNA fragmentation, increased caspase 3/7 activities and up-regulation of p53, Bax and down regulation of Survivin confirmed the proapoptotic effects of the compound. Significant inhibition of HSP complex related genes were also observed in SKBR-3 and MDA-MB-231 breast cancer cells. Conclusion: Overall results indicate that vernolactone can mediate its cytotoxic effects via apoptosis and modulating the HSP complex.