Our study is investigated the effects of Nelumbo nucifera root extract on HT-29 colon cancer cells. The anti-proliferative effect of 70% ethanol extract from Nelumbo nucifera root on HT-29 colon cancer cells was identified based on cell viability, Hoechst 33342 nuclear staining, apoptosis analysis, Western blotting and RT-PCR analyses. In our study, Nelumbo nucifera root extract inhibited the growth of HT-29 colon cancer cells in a dose-dependent manner. Concomitant activation of the mitochondria-dependent apoptotic pathway of HT-29 colon cancer cells by Nelumbo nucifera root extract occurred via modulation of Bax and Bcl-2 expressions, which activated cleavage of caspases-3 and -9. The findings of this study indicate that Nelumbo nucifera root extract induces apoptosis in HT-29 colon cancer cells, and this phenomenon is occurs via the death receptor-mediated and mitochondria-mediated apoptotic pathways.