Cell death mechanism triggered by aluminium (Al) ion was investigated at root apex of tobacco (cultivar Bright Yellow) and in cultured tobacco cell line BY-2 derived from Bright Yellow, focusing on VPE genes (NtVPE1a, NtVPE1b, NtVPE2, NtVPE3). Cell death was detected as a loss of integrity of the plasma membrane by vital staining with fluorescein diacetate (in root apex) and Evans blue (in BY-2), respectively. At root apex, the upregulation of gene expression of VPE1a and VPE1b was observed significantly after 9h of Al exposure in parallel with an enhancement of cell death, while the upregulation of VPE2 and VPE3 were observed later. Similarly, in BY-2 cells, the upregulation of VPE1a and VPE1b and the enhancement of cell death were synchronously observed after 3-h exposure to Al, while the upregulation of VPE2 and VPE3 occurred later. RNA interference (RNAi) lines of each of the VPEs were constructed in BY-2 cells. Comparative studies between wild-type and the RNAi lines indicated that both Al-enhanced VPE activity and Al-induced cell death were significantly suppressed in the RNAi lines of VPE1 (dual suppressor of VPE1a and VPE1b), but not in the RNAi lines of VPE2 and that of VPE3. Taken together, we conclude that the upregulation of VPE1 gene expression and following enhancement of VPE activity under Al stress cause cell death in actively growing or elongating cells of tobacco. VPE gene encodes vacuolar processing enzyme exhibiting caspase-1 like activity. Initiation of aluminium-induced cell death at root apex is strongly related to upregulation of VPE1 in tobacco. Study of the suppressor lines of VPEs constructed in tobacco cell line BY-2 indicates that VPE1 is essential for aluminium-induced cell death. Display omitted •Aluminium-caused cell death was investigated at root apex and BY-2 cells of tobacco.•VPE gene encodes vacuolar processing enzyme which executes programmed cell death in plant.•Aluminium causes upregulation of VPE1 and cell death simultaneously in both systems.•RNAi lines of VPE1 in BY-2 exhibit suppression of aluminium-induced cell death.•We conclude that upregulation of VPE1 by aluminium causes cell death in tobacco.