With wide use of nano-materials, it is increasingly important to address their potential toxicity to mammalian cells. However, toxic effects of these materials have been mainly assessed by the cell survival assays. Considering that mitochondrial morphology and quality are highly sensitive to the condition of the cells, and the impairment of mitochondrial function greatly affect the survival of cells, here we tested the impact of multi-walled carbon nanotubes (MWNT) on the survival, mitochondrial morphology, and their membrane potential in HeLa cells. Interestingly, although MWNT did not induce cell death until 24 hours as assessed by pyknotic cell assay, mitochondrial length was elongated and the mitochondrial membrane potential was significantly reduced by exposure of HeLa cells to MWNT. These results suggest that MWNT exposure is potentially harmful to the cell, and the mechanism how MWNT alters mitochondrial quality should be further explored to assess the safety of MWNT use.