Functionalization is an important technique to increase the solubility and biocompatibility of single-wall carbon nanotubes (SWCNTs). In this study, we investigated the cytotoxicity of four types of SWCNTs functionalized with hydroxyl, amino, carboxyl and polyethyleneglycol on MCF7 cells. These functionalized SWCNTs (f-SWCNTs) have insignificant effects on mitochondrial activity and ROS production in MCF7 cells at all test concentrations. However, explicit results revealed that all the tested f-SWCNTs could cause changes of cell morphology, induce cell membrane damage, decrease cell adhesion, and increase cell apoptosis. Therefore, this study shows the potential side effects of f-SWCNTs accompanying with the increase of dispersibility and stability in environment or serum (to prevent their aggregation), and highlights the need for further research to examine the potential toxicity of f-SWCNTs before they are used in the environmental and biomedical fields.