Multi-walled carbon nanotubes (MWCNTs) are increasingly used and many studies have already showed their cytotoxicity in different kinds of cell lines, while their mechanism is not fully understood. Mitochondria are the relatively sensitive organelle in response to the stress challenged by the exogenous chemicals. The study aimed to evaluate mitochondrial injury and cytotoxicity in mouse peritoneal macrophage cell line (RAW 264.7) induced by the water-soluble taurine functionalized MWCNTs (tau-MWCNTs) and pristine raw MWCNTs (raw-MWCNTs). The different concentrations including 0, 5, 20, 40 and 80 microg/ml for both kinds of MWCNTs were adopted. The cytotoxicity and the mitochondrial function were assessed after 12 h and 24 h treatment. The results revealed that both MWCNTs could produce significantly dose-dependent cytotoxicity and mitochondrial injury including the decrease of mitochondrial membrane potential, the release of cytochrome c from mitochondria and the increase of cytoplasm Ca2+ content. The activities of adenosine triphosphatases (ATPase) and succinodehydrogenase (SDH) of mitochondria were all inhibited after MWCNTs treatment. In conclusion, MWCNTs could lead to mitochondrial injury, which might be one possible pathway of apoptotic cell induction. The findings that tau-MWCNTs exhibited less toxicity compared with raw-MWCNTs support a useful approach to reduce the toxicity of MWCNTs by surface-functionization with taurine.