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).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.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.Overall results indicate that vernolactone can mediate its cytotoxic effects via apoptosis and modulating the HSP complex.