The residual metals were partially eliminated by purifying the pristine multi-walled carbon nanotubes (MWCNTs) with hydrochloric acid. The purified MWCNTs showed toxicities which were almost identical in magnitudes to that observed for the pristine MWCNTs. The experiments were conducted by cultivation of Arabidopsis T87 suspension cells in media containing MWCNTs. Contents for reactive oxygen species (ROS), catalase and glutathione were quantitatively analyzed. ROS and catalase increased and glutathione decreased were observed for the cells after the exposure to MWCNTs. The MWCNTs exposure also caused cell membrane disintegration and cellular organs structure changes. Our experimental data gave evidences to conclude that MWCNTs are toxic to the Arabidopsis T87 suspension cells and the overproduction of ROS is responsible for causing the toxicity.